There are a few things hidden into the code of RSE, such as the trait Cacophony (works the same as Soundproof), which suggests either they added extra things but never used them, or allowed for some forward capability. However, I doubt there was enough room.
So yeah, in answer to your question, it's gonna work pretty much the same as the Time Machine in GSC, where you could send your old Pokemon forward to D/P, but not the new Pokemon or moves back to RSE. It's the only way they can do it while allowing nearly complete compatibility. Plus it might add a few moveset ideas for the Advance gen series.