It's RKs that, together with Malaya and the Dutch East Indies, are the inconsistency, not the lack of a Protectorate of Bohemia & Moravia and the General Governorate for the Occupied Polish Region. Almost all other similar territories are handled by occupation laws and state core mechanics, as should all the aforementioned be were PDX to maintain consistency with established logic, logic that makes sense given how HoI4 is not designed to simulate sub-national administrative entities, nor does a good job of it when forced to attempt doing so.
Manchukuo and Mengjiang (Mengkukuo), IRL powerless rubber stamps for Japanese occupation, and India are the other inconsistencies, but unlike the others, they at least have some basis for existing beyond just "it's cool flavour and another HoI game (Darkest Hour) had them" or "meme focus tree can steal European colony".