So the issue is the companions ALSO have the tadpole AND a backstory? Do you just want them to be Blandy McBlanderson, small town fighter who wants to save up to buy a spear to fight large rats?
Also, name a game that has meaningful interesting story choices based on what you did in character creation. In general, its a few dialogue choices here and there, because branching story arcs require an absurd amount of work.
I don't even have an issue with the companions and their backstories.
I guess for me the way the story is structured right now makes it feel that the companions overshadow your player character. My personal preference would be if the story circled more around your character, and everyone else is an add-on that completes that story. Granted it doesn't have to be a hero's journey. Not every protagonist needs to be a larger than life Commander Shepard or Revan, they can be an Exile or the Spirit Eater, or even Hawke who is basically a boring human in the wrong place at the wrong time, and fail at every damn thing, but the story would still be and feel theirs.
Both you and companions have tadpoles, all of you have the same powers, all of you are special (which is fine), but the companions are now way more special than the generic PC.
I don't know what's the right way to do it, whether its making them less special or your PC more, or even going in another direction. Heck maybe if they didnt have tadpoles and you did, then it would already be different. I.e. you'd be saddled with something similar to a spirit eater curse.
Or maybe Larian has something else in store for us and we are just complaining for nothing.
