I think the issues is that at certain points in the story, the MSQ is serving the Trust system, instead of the other way around. I think it was in 6.3 or 6.4, where Thancred just shows up just before the dungeon, because otherwise you wouldn't have had a Tank role. After the dungeon is over, he just leaves instantly.

The Trust system on its own is great, but NPCs just popping in/out because of it is kinda terrible.