They are. You have 2 kingdoms. Each has it own history and culture. They have their own laws.
As the guy in charge you may decide that the people from Kingdom X should now belong to Kingdom Y. It is not just a flag change. Its a complete realm change.
If all you want is a new name you can use the DLC that lets you change them.
If you want the flag and history... you will have to live with the consequences of your decision.
There is a difference between realm laws and crown laws.
Crown laws apply to a specific title.
Realm laws apply to your entire realm, regardless of your titles. As you will see, when you play a count or a duke you still have centralization settings because they are a realm law. If centralization was a crown law, you wouldn't have the ability to change it, or even see it, if you weren't a king.
Also, if you switch between the king tabs you will see that there are NOT different centralization settings for each kingdom. If centralization was tied to the kingdom, then you would have different settings for each title. This is not the case though because centralization is a realm law.
If I change my primary crown title, this should only affect crown laws, not my realm law that is independent of any kingdom title.