I've thought about this more and my mind went to Fallout New Vegas. It had companions with quests too but they were overall unconnected to the main plot as well.
Not quite true - Obsidian tend to tie their companions to the main story as well - they tend to represent factions that we will interact with.
I think the advantage those companions have: is that they are companions. Story revolves with PC in mind, and companions are made to be skippable.
BG3 has companions, who are also playable heroes with super important driving plot to the story. The result is that during the you do play out stories of your companions, rather than your own.
I don’t think it is “freedom” vs “story” but that one hasn’t been designed to fit the other. It feels like we have a fairly rigid story, that than Larian is desperately trying to keep telling regardless of what player does. I think Tim Cains RPGs (fallout, arcanum) are great examples of more organic, system heavy games.
