Definitely with OP on point 2 re: Halsin and the goblins.

I actually really like not having the main character be the most Extra Special Snowflake that Ever Snowflaked, I think it's a really nice change from a lot of modern RPGs, and gives the game a fresh feel. It also helps with making the original ship crew feel more like a unit and helps me invest in all of their survival and stories. That being said, I really like OP's point 1.3, though I'd be perfectly content with a written prologue that matches the custom character creation choices—having a glimpse of normal life would help anchor the player's attachment to the character. It would also get around the impression that they just came into being the second they were nabbed by the mind flayers.

Perhaps another good compromise would be to use dialogue with other NPCs or the narrator's voice to let the player steer who their character was before the game started, without clogging the plotline with it or requiring more cutscenes or playable areas. It does this to a certain degree already, of course, but having a sort of "who were you before it all started" question from the NPCs would also balance those interactions where the player character asks them questions about their background but they don't ask anything back.