I just want to stress that me writing "Larian doesn't care about the story" is a bit provocative way to frame it. If I were to write it in a more nuanced way, I would say that Larian's design philosophy emphasize experiment and exploration. They seem to put player freedom at the highest regard when designing a game, and are willing to "sacrifice" story integrity to do so. And it's not necessarily a bad thing, I'm sure a lot of players like this design philosophy. I do wonder though (and I hate being that This-isn't-Baldur's-Gate guy) whether most BG players played this game for the same reason. If so, BG is kinda restricted and not a very good choice for this game style.
Except they are ruining experimentation and exploration by not rewarding players for it. What's the point if the result is the game breaking or not acknowledging your choices with pertinent NPC interactions?
They certainly haven't made their job any easier when your party contains multiple story characters. Each exponentially increasing the possible outcomes. You should be able to select one companion then find, interact with, and gain and understanding of each other companion while on the ship and then save only one of them in the escape IMO. This would cut down the amount of flags required.
