They were kind of setting up for the movie with that, the alternate world from Amestris is supposed to be our world with people who are doppelgangers, like there is an Amestris and our world 'version' of Ed, and both worlds are kind of like portals into another... when both versions die, their souls switch sides and are born again with no memories of their past, which is why human transmutation creates a homonculus, it drags both souls onto one plane and forms them into a different being...? the italic part is speculation on my part, but I think it works...