One Issue i need to fix is that the puppets keep their focus trees and national spirits, but im currently working on it.

The released states can still form formables. (Ostafrika for example forms East Africa and Kaukasien forms the North Caucasian Emirate).
You could either lock them out of the decision (make the decision for independent sates only or for player only idk) or you could just create separate tags for the RK's. That would also help you with your former problem (National spirits)

Its been such a long time since ive touched the mod, but i had thought that id already did that. I might take a look at updating it in the future