All true but all of these (with perhaps the gith encounter as the only exception) are not really big part of the story and are very similar to companions quests in other games. They are more extensive, but I think it's a plus rather than a minus. My only real issue is with Wyll's case, that gave me serious Dos2 vibes. It wasn't as bad as in dos 2 (let me remind you - you meet the dreamer and than the Red Prince not only takes over, you don't even hear what they Re talking about and just stand like a dofus until they are done). Still, I think, again, that the problem here is with event flags. The game should accommodate the fact that you are the main character better, and let you more choices in these cases.
Like I don't mind them having their own little tangents and stories. What I mind is that our PC doesn't under any circumstance interfere in any meaningful way - like, you either have a) yes, kill them and b) no, let them live, where are the other options? Like 'let's question/torture this mofo' where our chosen backstory could play a part in it. For example - a criminal could say, 'let's torture them, cut off their fingers one by one, get more info out of them' meanwhile an acolyte of a good god would be like 'let's do it quick and end their suffering' (if you choose to question and then kill someone). There are so many ways our PC could meaningfully interject aside from: yes or no (and sometimes the very rare maybe).
And since our companions are always supposed to be watching us and judging us, where are their little interjections for when we do something they wholeheartedly disagree with? Like you see that they 'approve'/'disapprove' but it would be nice if they actually said something meaningful that would point as to why that is. Like as of now, at best, they throw some snarky one liners at you.