The question of separate budgets isn’t really relevant. Larian sets their budgets how they see fit, and if not one way they could always do it another way. They have that choice. Furthermore, every feature in every game comes at the cost of some other feature. That is just a reality of prioritization and scope management. It is also important to understand that budgets are allocated based on expected return of investment. If a feature is scrapped it doesn’t necessarily mean that money will just be reallocated if the sales are expected to diminish. I’m not saying that is what will happen here, just that it is more complex than the impression you seem to have.
A more relevant question is: how much extra work goes into making origin characters as opposed to normal companions? The origin personal quests are still in the game regardless of who your main character is. What you get from playing an origin character is a bit of extra content that comes from seeing these quests ,and maybe some others, through their perspectives. How much work is that? Impossible to say at this point. Larian seems to think it’s worth it, and we can assume that if they found origin characters in DOS2 were a waste of resources then they wouldn’t be doing it again.