Just like each of the Great Houses differ much in it's culture, architecture, ways and views on life from the other Great Houses, the Seventh House of the Dwemer was indeed different too, but still it was a Great House consisting of the same race that populated the other Great Houses.

Some sources describing the Dwemer as an ordinary Chimeri Great House:
The Real Nerevar by a Telvanni retainer - "When the Dunmer followed Veloth to Morrowind, they were many warring clans, with no law or leader in common. One Dunmer warlord, Nerevar, had the ambition to rule all the Dunmer. In that time, House Dwemer were great enchanters, so Nerevar went in secret to a Dwemer smith and asked for an enchanted ring that would help him. The ring gave its wearer great powers of persuasion; for safety, it was enchanted to instantly kill anyone who wore it except Nerevar. The ring was called Moon-and-Star, and it helped Nerevar unite the various clans into the First Council. Later, however, disputes over religion divided the Council, with House Dwemer and House Dagoth on one side and all the other Houses on the other. Dwemer and Dagoth invited Orc and Nord clans as allies, and held northwest Morrowind, while Nerevar mustered the other Houses and nomad tribes and marched to meet the Dwemer-Dagoth-Westerner forces".

The War of the First Council by Agrippa Fundilius - "The War of the First Council was a First Age religious conflict between the secular Dunmer Houses Dwemer and Dagoth and the orthodox Dunmer Houses Indoril, Redoran, Dres, Hlaalu, and Telvanni. The First Council was the first pan-Dunmer governing body, which collapsed over disputes about sorceries and enchantments practiced by the Dwemer and declared profane by the other Houses."

As we see it, the Agrippa's witness supports the previous one of the unnamed Telvanni retainer who hadn't named the sources of his text. The Telvanni could actually be that "Dunmer" source of Agrippa's work as well as he could be a straight witness of the events himself, or he could use just the same sources Agrippa used were he living later. Anyway, since Agrippa's chronicle is based on the various Imperial and Dunmer sources, and since it supports the Telvanni's chronicle, we can assume that it is possible that the Telvanni chronicler is credible. Both authors speak of the Dwemer as if they were of the same race the Chimer were, and thus the Dwemer were a Chimeri Great House who formed the First Council.

The Lost Prophecy by Gilvas Barelo, Abbot of Holamayan - "The 'unmourned house' could be either or both of the lost Great Houses of the Dunmer -- House Dwemer and House Dagoth" as he says it regarding the lines 6 and 7 of the prophecy: "Star-blessed hand wields thrice-cursed blade, To reap the harvest of the unmourned house". Indeed, the "unmourned house" could mean here not only House Dagoth, but the Dwemer too.

Barelo continues in his Seven Curses work - "Lines 1-3: Ambiguous. May refer to the impiety of the god-mocking House Dwemer, or the treacherous diplomacy of the subtle House Dagoth, or both. House Dagoth, however, was reviled as oath-breakers for their treachery at Red Mountain".

This generic dialogue repeated by many different NPC on the War of the First Council asked in the Third Era Morrowind tells us that the views on the Dwemer as the Seventh House are also common to the folk consciousness and is not something known by scholars only - "The first government of all Morrowind was called the First Council, comprised of representatives from all the Dunmer Great Houses. This First Council mobilized to suppress a civil war. A rebel house, House Dwemer, joined with Nord and Orc clans to invade northern Morrowind. The rebels, invaders, and a traitor house, House Dagoth, were finally defeated and destroyed at the Battle of Red Mountain. See Agrippa Fundilius' book, The War of the First Council, for a more complete account".

And so on. As you see it, both the written sources and the common people make no difference between the Chimer and the Dwemer, moreover they even underline that they are the same race ("rebel house, House Dwemer, joined with Nord and Orc clans"). None of these sources speak of the Dwemer as a separate race. And none of the foreign nations have ever been called a great house by the Chimer and the Dunmer. "House Nord", "House Altmer" or "House Bosmer" - sounds really weird. Still there are also sources that made us believe that the Dwemer were a separate race like the Pocket Guide to the Empire, 3rd Edition: All the Eras of Man by the Imperial Geographical Society and the Anuad Paraphrased, but as you see it, they are mostly non-dunmeri ones - they are the sources of those who's ancestors have never lived with the Dwemer in one country. But the major source that actually made all the questions fade is, of course, Yagrum Bagarn himself. Bagarn says it several times "my race", "our race", "Dwemer race" and it surely made us believe that the Dwemer were such a separate race. So credible he was, but pay your attention that he also mentions the Dunmer, saying not a word about his contemporary Chimer, in spite of the fact the Dunmer were not present that time yet - he spoke those words to a modern 3rd Era listener. This made me think he used the word "Dwemer" just the same way he used the word "Dunmer" in those dialogue lines, i.e. to make it more comprehensive to a contemporary Third Era listener. I.e. to us. The reason of such a separation of terms regarding the same race will be discussed further on here.

Regarding the word "Dwemer" I also recall the words of our old friend Hasphat Antabolis - "Elves use the term "Dwemer," connoting variously "deep-delving," "profound," and "close-counseled"; Imperial usage is "Dwarven," derived in fable from the affectionate regard of the Giant races for their "little" Dwemer friends".
I have marked those words because I think it is the most accurate meaning, i.e. the "wise elves". Why the wise? What was the difference they had with the Chimer? Well, here it's time to speak of Julianos.

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House Dagoth retainers are said to be Chimer by all the sources. It is a generally accepted fact. But whom do they look like more actually - the Chimer or the Dwemer? I think this is a witness that they were all one race actually with no differences in their appearance, but only differing in their outfit traditions though not that dramatically. Shave a Dwemer and you will see a Chimer .

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Some crucial remarks on the Velothi Exodus. Among all the lore sources there are only a few stating that the Velothi schism's reason was initially the Daedra worship. It's the Daedra Worship: The Chimer by Phrastus of Elinhir - a completely pro-altmeri Imperial scholar who's works are much doubted by the scientific community, and The Fall of Trinimac by some "Faithless One". All the other sources like the Exodus from Summerset, the Changed Ones, The True Nature of Orcs, Veloth the Pilgrim and other tell that Veloth and his followers were cast out because of the disagreements about the Aldmeri policy - Veloth was proclaiming that the Aldmer were scorned by those who were blind to the corruption and spiritual bankruptcy at the heart of their society, he disagreed when the "religion of the people also changed because of this change in society: no longer did the Aldmer worship their own ancestors, but the ancestors of their "betters." Auriel, Trinimac, Syrabane, and Phynaster are among the many ancestor spirits who became Gods". So it is no surprise Veloth revolted, and it was Trinimac who tried to stop his movement literally or by the means of those who worshipped him by "crying and shaming the ancestors" of the modern Dunmer and even taking "the Missing God's name in vain, calling His narratives into question" - whatever it was, it was only after the social agenda disagreement when Boethiah interfered. So the reason of the Velothi schism was not in the Daedra-worshipping nature of the Velothi teachings - the Daedra came a bit later and simply split the outcasts in two. Looking at the map of the Daedric shrines shows that the process was not instant, it started during the Exodus but massively the Velothi became Daedric Daedra worshippers in Resdayn only. I'll speak of it later here. So, after Boethiah revealed the Tri-angled Truth the Chimer began to abandon the Aedra worship - "Most traces of Akatosh disappeared from ancient Chimer legends during their so-called 'exodus'..". Some sources even say that Boethiah's interference happened at the very end of the journey. Whatever it was in reality, it is only up to each of us what version to believe in. What is worthy of noticing here is that the Veloth's image considered to be holy by the Temple depicts much more a Dwemer than a Chimer we got used to:
Look at that beard and purely Dwemeri features. Yes, we have seen the spirit of Veloth in Deshaan when we were chasing Magistrix Vox, but you know it as well as I that the spirits can appear very differently and their appearance can change. Many of them can't distinguish the mortal world from the otherworld, the other can't focus, the third lose their memory totally or partially - so, the Veloth's spirit and his appearance is not a credible argument to anything. It could also be used a random model by the developers if they decided not to make a separare model for Veloth like they did for Sotha Sil. I guess it can be true since even Almalexia's model is just a simple Dunmeri woman's model in some uncommon clothes and effects. So, yes, it's just another point of view, as credible as the holy images used by the Temple - I believe those images much more then the 3D model of Veloth we saw in the vanilla ESO in Deshaan. So, the Velothi people changed. Here is the time to remember the two other sources that will give us a bit different translation to the words "Dwemer" and "Chimer":
1. Hasphat Antabolis - "Elves use the term "Dwemer," connoting variously "deep-delving," "profound," and "close-counseled"; Imperial usage is "Dwarven," derived in fable from the affectionate regard of the Giant races for their "little" Dwemer friends".
2. The Savants' Notes on Vvardenfell - "Chimer -- literally "the People of the North," an archaic and poetic usage -- were the Elven tribes who followed the prophet Veloth out of the southwest of Tamriel to settle in the lands now known as Morrowind. Dunmer fable says that before their skin turned dark with the Curse, the Dark Elves were known as the Chimer".

Just like the Cantemiric Velothi of Argonia, the Dwemer could be the Profound Velothi of Skyrim. And here we come up to possibly the main riddle regarding the Dwemeri origins - was it Resdayn their homeland or was it.. Skyrim?

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In conclusion I'll just gather all the things I have written above and will show a brief picture of what I believe in based on the existing lore, it's contradictions, gaps, material evidence, books, dialogues and so on.
1. The Dwemer were the Aldmer whom Veloth was leading in the Exodus. Later those Aldmer split in two groups - the Daedra worshipping Chimer and the "secular" Julianos "worshipping" Dwemer.
2. Veloth revolted against the policy of the Aldmeri society. He and his followers were mocked much and persecuted. The major part of the society even began to mock at their ancestors. The confrontation made the Velothi leave their kin and move towards Morrowind. The journey brought them to Skyrim.
3. Either in Skyrim or at some earlier point during the Exodus a part of the Velothi changed their views to the Three Daedra cult, another part (the Trinimacists) became the Orcs. The third part, as I think of it, became the Dwemer - they were changed into Chimer too, but heeded the initial teachings of Veloth. Just like later the Chimer-Ashladers changed into the Dunmer in spite of the fact that they were loyal to Nerevar, they refused the betrayal of the Almsivi and kept faith in the Three Daedra. At this point the Velothi devided in two groups - the Daedra worshipping "People of the North" (Chimer), or, as I think, "Northern Elves" since there is that "mer" part, who came from the Dunmeth pass to Morrowind, and the "Profound Elves" (Dwemer). Both the Chimer and the Dwemer did not stop in Morrowind - some clans settled in Skyrim, the other continued and settled in Morrowind, the third, the Cantemiric Velothi, even reached Argonia.
4. The teaching of Saint Veloth initially was not about the Three Good Daedra - it was some Aedric cult devoted to Julianos and possibly Akatosh. The beliefs began to change to the Daedra worship later during the Exodus. Not all of the Velothi accepted such changes - the Dwemer and the Dagoth seem to be the only ones who kept heeding the initial faith. Veloth was used as a banner each time the Velothi changed their religion - he was credited as a founder before the Exodus, during the rise of the Three Good Daedra cult, during the Tribunal Era and during the New Temple - each of the three Dunmeri religions claimed Veloth as it's prophet in spite of the major differences between them, in spite of that Anticipation-Reclamations thing, etc.
5. I believe that the Ancient Tales of the Dwemer by Marobar Sul described in many sources like a Dwemer History and Culture by Hasphat Antabolis whom I respect really much, as a total fiction is actually a serious historical document. I believe that those tales describe the early Dwemeri times when they were not that developed yet, when Argonians were indeed living in the Dwemeri lands even before the Dwemer came there. It's no surprise to me that the publisher notes speak of many resemblances of those tales with the Dunmeri ones - they were one nation by the time, the very same people. I suppose that after their defeat the Dwemer became the most slandered people. Their history was rewritten, their image was spoiled, they were stripped off their ancestral ties with their kin and would have been totally erased from history if not the material evidences they left. Their fate is so much similar with House Dagoth with only one difference - the Dagoths have never been called the other race. I suppose it's because their children were distributed among other houses -unlike the Dwemer who vanished entirely. Since the Tribunal were unable to destroy the Dwemeri traces entirely, they began putting the Dwemer into the same row with the other races, though the folk memory and many sources still name them House Dwemer.
6. The Dwemer are also never described as slavemasters anywhere except the only episodes with the Falmer. They've never enslaved goblins, Chimer, Nords or anyone else, but the suddenly decided to enslave the Falmer - this is what we are offered to believe in. The Falmer were another religious fanatics just like the Chimer, so it's no surprise Gelebor said that the two nations had complicated relations. And it's no surprise to me that just like the Chimer, the Falmer accused the Dwemer in the worst things their minds could imagine predictably leaving no space to preserving the Dwemeri point of view. I don't believe that the Dwemer required any slaves at all. I suppose they accepted the Falmer as brothers and junior assistants, but the ungrateful religious fanatics betrayed them themselves, and did things like the ones described in the "fictious" Ancient Tales of the Dwemer VIII.
7. The Dwemer were just the Seventh House of the Chimer. Just like we say "Telvanni mages" we don't mean the mages of the Telvanni race, the Dwemer were likewise just the name of the Great House. All the lore tells us that they were smart, wise, industrious, honorful and highly developed but yet tolerating and friendly culture to those who were living worse, but the same lore describing them that way always makes a conclusion like "The Dwemer were raided by the Chimer. What a scums those Dwemer are!.."
8. Since the Dwemer are the Seventh House, I believe that all the lands from the island of Stros M'Kai, Hammerfell, Skyrim, Morrowind and Northern Argonia can be treated as the Dunmeri ancestral grounds. Have a look at the locations of the Daedric shrìnes in Tamriel - I believe they were all built by the Chimer, the group of the Velothi who turned to the Daedric ways. The quantity of the ruins at certain locations shows a possible way of Veloth's Exodus and the quantity of those who became Daedra worshippers.

Thank you all for reading, I hope it was interesting and gave you the reason for your own thoughts to come to your minds. Have a nice day, guys, and see you around!

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Thank you for a good question, @Ratzkifal. My answer will be based on facts I'll explain in details below (with some extra information you or other readers might find interesting), in short it's four points here:
1. It is possible to link the Heart to certain groups of people of the same race without effecting the rest of them.
2. We don't know the real reasons why the Rourken left and the status of their connection to the Heart and to the rest of their House - all we know for sure is that they fought back to back with all the Dwemer and all the Chimer against the Nords and that they settled in Volenfell 4 years after the First Council was formed, being the first evidence of the long Dwemeri expansions to the west to reclaim Skyrim territories and conquer Velonfell ones after the war in Resdayn was won.
3. Signus' Dwemeri lockbox that was designed to be opened by a sample of Dwemeri blood only, was opened without it using the samples of other Elven races combined with the Dunmeri one among them.
4. We don't know the principles of neither Kagrenac nor of the Tribunes they used to manipulate the Heart that makes impossible to find truth of why the Dwemer disappeared while the Chimer did not. The truth is that, since we don't know those principles, since the Dwemer disappeared alone, and keeping in mind the facts that I have already given combined, the Rourken and all the other Dwemer clans did not necessarily have to be a separate race to vanish leaving the other Houses alive.

In order to answer your question we have to know why the Rourken left in reality, what were their relations with the Vvardenfell kin and what exactly were the settings Kagrenac used linking his kin to the Heart. All we have today are just the in-game speculations of different scholars. What do we know for sure are these facts only: all the Dwemer united with all the Chimer, they drove the Nords out of Morrowind and formed the First Council in 1E 416. In 4 years, 1E 420, the Rourken settled in Volenfell, and yet "in the decades following the establishment of peace between the Chimer and Dwemer, Dwarves of Clan Kragen began to seek new holdings beyond Resdayn", though Neramo is much more honest here regarding the reasons of their departure - "It's unclear precisely what appealed so much to the Kragen explorers that it was worth settling among the hostile Nords, but in spite of regular attacks by the warlike Men, their city flourished. So much so that it encouraged other clans to expand their own holdings to the west".

Personally, I think it was the continuation of the war against the Nords this time on their territory - a common thing when you fight off an invader, something that the modern Ebonheart Pact military command is too dumb to understand launching no retaliation attacks into the Covenant and the Dominion lands after the invasions they have performed recently into our territories. We can also recall that book describing the Aetherium Wars I mentioned in the OP - the Dwemer lost it's Skyrim cities to the Nords and reclaimed them later. In order to reclaim them they had to start out from somewhere - I suppose it's another description of the same event of the Dwemeri march to the west as soon as they liberated Resdayn. Why only one Great House performed it? First of all, they might have been not alone in that. Secondly, as Athal Sarys said it his book - "Your beloved Five Hundred Companions may have driven our ancestors from Skyrim, but that was then. This is now". Aside his propaganda, what ancestors did he mean in that line - Dwemer, Falmer or both? There are no references to the Falmeri connections with the Chimer at all, but I've already given many of them regarding the Chimeri connections to the Dwemer and Skyrim both combined and apart. But it's a completely other story.

Anyway, even these facts on the Clans Kragen and Rourken fade when we get to the Falmeri lore I mentioned up there that states that the Dwemer had been living a much developed life in Skyrim centuries before the Kragen founded the very first and the main Dwemeri city in Skyrim. A pure contradiction. So, I suppose the statements about the Dwemeri internal disagreements regarding the Chimer are not that credible. They have united once to fight back to back against Nords, but refused to live in peace?.. Why?.. That's not that credible to me, I don't believe it and the lore gives no answers living us to speculate. So, it is possible that the Rourken were not that distant from the rest of their kin as those authors think.

Secondly, indeed, in every line regarding the attunement to the Heart the lore states that Kagrenac was working to benefit all the Dwemer, not just some group of them. I treat it the way his research was conducted for the benefit of the Seventh House only leaving the other Six Great Houses beyond. The possibility to link such a group does exist and it reminds me of the idea of Dagoth Ur to make each of his House kin immortal by linking them to the Heart - ".. will you share the Heart with your followers, as I have, and breed a new race of divine immortals?". He also says regarding his kin - "The Sixth House .. will become, as suits their abilities, either holy warriors or priests. Their .. joy and liberation is to enter even-more-deeply into the profound enlightenment of the divine dreamworld". We also remember those quests both in TES III and the ESO showing us that only the descendands of the Sixth House were effected by Dagoth Ur's powers. And the source of those powers was the Heart he used to communicate through dreams and to grant immortality to his kin, other Dagoths. That was also his claim towards the Tribunal that they did not share their power with the rest of the Dunmer.
Some references on how do the Ash statues work:
Diviner's Journal - "The woman I divined in my dreams has come to us, and the purity of her heritage is beyond even our most hopeful expectations".
Guardian's Decree - "The Wakener has taken the pure-blood into his sanctum".
Wakener's Sermon - "The diggers whisper that they can feel the call of the ash statues drawing them closer, but it is not their rude blood to which the statues sing. I have seen revelation in the eyes of the blood heirs as they held their birthright. True understanding. Through them we will shape the world into its ordained form. Find those whose bloodline speaks to this place. Their awakening is nigh".
Nevena's Diary - "I know what it is. I know what I am. The naked stone in my hands was electric. Jolting me awake and out of the hollow stupor I was cursed to live through all this time. The Temple thinks it can bury the truth, but the only ones they are blinding are themselves. Our legacy lives on. Our House will be made whole again. It's been calling to me all this time, I just couldn't hear it.".

So, it's possible to somehow share it not just among the House kin only, not just race, but also among simple followers. But even if the key is blood, then we have to remember the "trick" performed by Septimus Signus - "Dwemer blood can loose the hooks, but none alive remain to bear it. A panoply of their brethren could gather to form a facsimile. A trick. Something they didn't anticipate, no, not even them. The blood of Altmer, Bosmer, Dunmer, Falmer, and Orsimer. The elves still living provide the key". He thought it was a trick to overcome the Dwemeri lockbox, but I suppose it just worked as it was intended with only the Dunmeri blood being enough to open it. Why it was not a trick? First, because only the Chimer shared a great similiraty in their appearance with the Dwemer, while all the other Elves were yet truly other races sharing nothing common but ears with them. Secondly, because I don't believe the Dwemer made a rule and were that dumb to leave a space for "tricks" to avoid that rule. Finally, because the lockbox actually opened without the Dwemeri race's blood but with the Dunmeri blood among the samples. This makes me believe that the Dwemeri blood is nothing special there and the reason why all the Elves disappeared has nothing common with the blood of separate Dwemeri race.

Regarding the mechanism of the disappearance of the Rourken in case they truly had no connection to the rest of their House, I think it happened due to the same reasons the rest of the five Houses (the Chimer) turned into the Dunmer including the Ashlanders who were the least deserving that Azura's curse among all the Chimer and had nothing common politically with the Houses. Yes, I don't believe that Azura cursed the Chimer turning them into the Dunmer - she has never done anything like that neither before nor after it (unlike that stubborn dummy Mehrunes Dagon who performs the same mistake invading Nirno on and on). So, I think it's just Vivec's and his Temple's propaganda to cleanse themselves for what they have done by using the Tools of Kagrenac - the Dunmeri appearance is the direct consequence of the Tribunal's manipulation with the Heart. None of the Chimer were linked to the Heart except the Tribunes, but somehow it had it's effect on all of them. I suppose, were some Chimer in the Outer Worlds during that moment just like Yagrum Bagarn, those Chimer would have not turned into Dunmer too. As we can see, somehow Almalexia managed to negate the "Azura's curse" completely, Vivec - partially, and the most powerful mage among them could do nothing to stay Chimer in his appearance. So, was it Azura that weak or.. Or was it the consequence of the Tribunes' actions? I believe that the only thing Azura did in reality was writing the prophecies and bringing Nerevar back. All the other things she might be blamed for today seems to be the consequence of the Tribunal's policy to increase the numbers of their laity and stay powerful, suppressing Daedric cults and other heresies. Nonetheless, it's a completely other topic, and all we are left to do since the lore does not give us the details is to observe the events based on the reasons and consequences.

Good points, @Ratzkifal, and a good addition to my theory regarding it's controversial approach. The thing I liked much was about the way the Velothi used to travel to Morrowind, i.e. across Hammerfell - that is the idea that somehow has never come to my mind before, actually, and now I have the reason to think it over. An interesting and quite credible idea, indeed. Aside quite a few things that you have perceived wrong in my original posts (perhaps, it's because of my bad English), you have posted a good opinion, and except that part about Veloth in Hammerfell, the interpretation you have posted is not new to me.

The thing I disliked is that your entire response was reasoning your denial of my thoughts entirely without any reasoning to support my idea. It's quite a rare thing regarding such topics for any wise man, so I suppose you had something personal. Though I don't remember if we had any disagreements before. Anyway, you might not understand what I mean if and until we switch the roles and I show you another perspective of it. Both of our opinions are based on the interpretations of the lore, but I perceived your post as if it was implying to some truth intended to break an idea that claims to be truth. I have written it in the thread's title - "a theory" to make it clear that it is just an interpretation, an opinion, and not even a thing I believe in personally. Personally, I operate possibilities, and on almost each thing like this I have different versions based on the lore, each with it's pros and cons, and basically I stick to none of them. Of course, this theory have many cons - it's a theory after all, not Truth One and Only.

Earlier I have published here another theory I have invented, a much bigger one, I'm still trying to find time to correct and improve it - that one does not touch this "Dwemer & Chimer are the same race" idea at all, moreover, it contradicts this theory. So, will you launch another crusade and point at that contradiction between the two of my own theories? Since this thread is dedicated to this theory only, all the facts I used were interpreted according to it's very idea only without pointing at other interpretations. Perhaps, I really should have given controversial reasoning there too, indeed. But to me it was all too obvious to write, and to be honest, I was expecting the readers to help me improve it somehow, point at some pros I have forgotten to mention, because argueing it is something I can do quite well myself as well as anyone who knows the lore quite well. It's not that difficult.

Everything I create regarding the lore is intended to make players see things in a bit unusual way to them, to create the reason for possibly new thoughts to come to their minds. I've been studying TES lore for decades almost from the very beginning, so it's really hard to impress me with anything there. But I have to admit it, you did it with that idea about Veloth in Hammerfell, thank you! I know you're good at the lore study too, Ratzkifal, no need to prove it to me. So, I hope you understand that this theory is not the result of my ignorance or my miscomprehension of the lore - it's just another interpretation that came up to my mind, and I decided to share it since I have found nothing like that on Internet. So, let the articles you wrote be a part of this theory, since I haven't written them myself. You did a good job, and I thank you for your time. It will surely let people think over this theory on their own and, perhaps let them formulate their own views on this topic.