Have installed now central, and have no of this issues because for the time being only updated central without moving all the stuff from root P3D.
In a way don't see problem to keep it within to structure as it was, the only thing is maybe space, but this can be solved to clone your disk to bigger size.
so if you only change without migration all stuff there are no strange issues, only thing have to correct is insert point, and scenery.cfg was same as before.
did made for safe some copies of all cfg's in case of problem, could paste it back.
have also read somewhere that Global Base should be for the time being left in P3D Root, because the change of default textures that are being replaced.
rgds