Yeah the concerns there are valid, and yes I have thought about the same. It would require some new iterations, but mainly tuning for experience and the levels you meet along the way. And yeah after all it is a suggestion, just thought i'd mention it since it would lead to a steadier flow of how you use your pokemon and that the progression is always going forward, not backtracking for each region.
And as it stands with only two regions, yes that can prove to be a problem. But then again it doesn't have to be specified like that, there could be other implementations of this, where the two first regions provide more levels than the next regions given. I mean yes level 100 has always been the standard super end game level of a pokemon, could be 50 for the two regions we have now. And then you could gain 10 levels per region afterwards.
Without seeing any code or knowing how they have programmed it, I won't know how much more work this would be or if it is desirable at all :)