Is that why the anime has confirmed that Palmer is Sinnoh's Tower Tycoon, rather than Johto's? That certainly wouldn't make it easier for HGSS players to fathom his presence in Johto.
Either way, they have made it so the anime only has to do 1 not 2, it will either be in Johto or in Sinnoh. Personally, I think it will be set in Johto, just like it is in HGSS, but that is my personal opinion of what will happen and nothing more, I'm not stating it as fact.