Star Wars the Old Republic has a similar situation. Due to player choice, with important characters being able to be killed off if a player so choses, what happened was that killable NPCs simply couldn't play a large role in future stories. Players were frustrated because they always have similar unkillable NPCs with them in the main story, but the reality was, if you didn't, you'd have to have generic new characters for every new expansion.
BG3 as you've mentioned has fallen into a similar situation. It's why I've said that Origin companions simply aren't necessary to play as, you're getting a bit more flavour sure, but they cannot be integral to the main plot, because you're not forced to take them with you. It's the unfortunately reality of complete freedom of choice, you're making the overall story shallower because it has to be.
It's why the box magically appears in your hand if you don't recruit SH. Similarly, the Emperor is absolutely integral to the story, and that is why you have people wanting to kill them early, ignore them, but we're not allowed to, because Larian quickly realized "uh, if we let them do something, they'll do it". It's just how people are.
I don't think it's necessarily a bad thing, but it's the reality of how they've made the game.
