I don't believe you are getting the point, I believe the current system they use to switch between regions is done by a script and code that checks for the rom, if you don't have the rom the scripted npc won't let you leave. This is a lot easier than adding flying between regions, to do that they would need to create new code for the Map UI to check that emerald is there so they could emulate its map, and I'm sure add checks everytime you fly somewhere to make sure it is emulating the right rom.
Thats just speculation, bottom line being, its never as simple adding things in as you may think.
If its not a simple process why have them waste time making something you can already do in about a minute by flying to a port city anyways?