Why did the NPCs all submit to letting the Bhaalspawn assume leadership in BG1? The same reason. Nobody in the party knew their heritage until towards the end of the game.
To be honest, BG1 doesn’t have many choices to make. As such I don’t think there is much clash of what companions and what you would do. Imoen definitely isn’t a leader, so it makes sense she sticks with big brother. Khalid and Jaheira were tasked with keeping you safe, and they point you toward your next objective, so in a way you the player are to follow they direction. Actually, if I remember well most early companions tell you where they go and it just happens to be the place you should be going it (neat, organic guiding through the open world!). Minsc/Edwin send you on another quest, and will turn on you if you won’t do it within a short period of time. Perhaps, simply lack of companion content didnt lead to question, why they would follow PC - just another meat bag to add to your squad.