One of the changes that Royal made that really annoyed me was, once securing the route to the treasure, the palace level goes up to 100% instead of only 99% like in vanilla. I also learned that reaching 100% in a palace doesn't even kick you out anymore. To be honest, vanilla Persona 5 handled the palace situation a lot better in this regard.
I have a feeling that the palace stuff is stored in the exe, so it'd be hard to change, but would it be possible at some point?
I hope I can have agreement that this is a rather unneeded change in Royal...