Well, first off, you can get transmute stones from Clockwork City. Its just from Asylum Sanctorium, same as with the other trials. ZOS usually locks transmute stones behind PVE group content, solo arenas, and PVP. Its only available for doing overland content during certain event rewards, so I'm not sure why stones would be available from anywhere else in CWC just because it came out as part of the DLC.
But there are other reasons.
Transmutation is a base game feature, not limited to the owners of the CWC DLC. While the only public transmutation station is in Clockwork City, all players can use the housing ones whether they own CWC or not. This is in stark contrast to Jewelrycrafting, which is a Summerset-limited feature. Jewelry stations are everywhere, but unless you own Summerset, you can't use them. So, sure, why not have transmute stones drop from places outside of the CWC zone?
We can even talk about ZOS' original intent for transmutation, where its pretty clear that they were responding to complaints about players running dungeons, trials, and arenas hundreds of times with no guarantee of getting the weapon/armor piece in the trait they wanted. But honestly, I'm not sure what point you are trying to make.
Are you seriously suggesting that we should make Transmutation limited to Clockwork City owners in the ability to obtain transmute stones?
Should we then restrict the ability of players who don't own CWC to use the transmutation stations as well?
Because no, I'm vehemently opposed to retroactively making transmutation more limited like Jewelrycrafting is.
Look at it this way; just because Sotha Sil (or his followers? IDK) created transmutation doesn't mean they created or even have greater access to the stones it's powered by. It's like if someone built an engine that ran off the friction if tumbling sand, they didn't invent sand, sand is everywhere, they just saw an untapped resource and found a creative use for it.