Having an assistant despawn a companion makes interacting with both systems a bit of a pain.
Why not merge them? Have your companion have the ability to be your banker, merchant, armorer or smuggler (if they have questionable morals). Requires the purchase of at least one banker, merchant or armorer respectively to do so though.
I was thinking giving the base game a non-combat companion by moving the CWC automaton rebuild quest to Morrowind that unlocks him as a very basic, non-combat companion. He is unique in that he can be spawned into dungeons, spawns in much faster as he has no inventory or weapons to look up, is invincible like an assistant, does not attack and can join you in dungeons/trials. Then scrap the smuggler NPC in lieu of 'Thieves guild smuggler network'. When unlocked your automaton (and later Ember) can do smuggling for you instead, given Ember is everything the smuggler assistant should have been. That way people that do not have High Isles can recreate their Smuggler as an Automaton (no morals) and later when they find Ember use her as a smuggler if they so choose.
It is also more practical that an automaton would follow you into a dungeon than a banker.
To get even more clever with this, don't have the automaton spawn in by the players request, but have it part of the dungeon / trial itself. It follows the group from behind and will stand at designated areas out of the way, just have a pathway in every dungeon, arena or trial that it follows (assuming the road ahead is clear, if the party has skipped a fight it will jump to the group and continue its pathing) and moves up with the group after every trash fight or boss encounter. That way nobody spawns in their Assistant, there is one assistant tucked away in the corner prior to every boss fight not causing noise on the screen, that has unlocked the entire culmination of the groups crown unlocks (bank, merch or armorer). No more will we do a 24 man HRC trial with 12 Tythis Andromo's running around.