So regarding DU, I'm skeptical that it was ever meant to be the default Tav. Getting random urges to attack a weird, evil mental construct is a far cry from what we experience as DU. There was no hint of it elsewhere in EA. Also I am very glad DU was not default because if it were, I'd never play the game. The level of darkness and gore imposed upon the character just would have been too much, and I'm sure other people would have felt the same.
As for the main topic of this thread, I suspect part of the problem is that Larian locked down the nautiloid opening sequence years in advance at some point months before EA, and as the story developed they couldn't give it a different beginning. Because if you think about it, once you know what the nautiloid we start in was actually sent to do, it doesn't make sense why they would attack a random city and take captives on what is supposed to be a specific mission with a specific goal.
Furthermore regarding the "It's fate" idea that Ido posits, I don't mind fate being a thing in fantasy stories, but it's really not a thing here. I'd buy it if it was like, each and every companion was vital to ultimately stopping this threat and they all had to play a part along the way. Nut that's not the case. You can play through this game solo and that doesn't really alter the ending.