I don't know if Larian had a complete and finished storybook before they started development, but from the interviews I've seen with voice actors, devs and Swen Vincke over the past years, it is clear that there were lots of important changes made during the development. The VA's didn't just follow a scenario, but they actually shaped some of their character traits. It may be so that this input is just the thing that makes the companions so intrigueing and likable, but surely this has a cost with respect to the original underlying story. Devs and graphics people had new ideas while the game was already in EA. In one interview they talked about Karlach beng entirely redone. Someone came up with this "cool idea" of an infernal heart and they thought that would be a really great change to make. Which it was ! Karlach is a great, dramatic NPC. Maybe the best of the lot. Wyll's story was completely altered , and so on..... All this improves the game in some points but must ultimately make other parts crumble.
So after all the cool changes were made, they should have gone to a new iteration and create a new storyboard incorporating the novelties. But, I can see that the scope of such an endeavour would be too big to do it "for free".
Well , it will be interesting to see if Larian keeps this same approach for its next game, which will be even bigger than BG3, or restrict changes on the way. Or do the iterative thing, which might be too costly.
