I tend to disagree with restricting options at character creation. Because :
- a) More customisation = better, in my view. To some extent, if people do shit (build-wise or lore-wise), it's their problem.
- b) Even if some combination sounds very off, there will always be someone somewhere who can justify a good backstory for it.
Currently, you can make many non-sensical combinations, and I'm fine with it. In a TT setting, that would fly.
This being said, there is the question of how Larian deals with it, as this is a video game and most of the GM-ing and writing will be fixed. If Larian has already made assumptions and written them in (like the Vlaakith-following Githyankis), then we probably can't ask them to remove that. We may ask them to write also for a non-Vlaakith-following Githyanki. That would be great.
But I think the best is not to prevent characters that would expose themselves to writing-clash, but instead to flag them. If you create a Githyanki Cleric that doesn't follow Vlaakith, when you choose a different god, there should be a warning "we have written Githyankis to be Vlaakith followers. Your combination will lead to you witnessing inconsistencies. You may venture forth this way but we don't recommend it".