I thought the same thing. They really don't seem to align with each other. Maybe X-Man/Legion/Apocalypse or whoever it is that warps reality separates the X-Men into their own distinctive universes.
Based on hints from Rosenberg, Logan and Scott mighn't be the only mutants left in 616. Presumably Emma Frost, X, Mystique, Rogue, Gambit, Kid Cable, Domino, Warpath, Cannonball, Shatterstar, Boom-Boom are left behind. And potentially more of the mutants that aren't attached to the Age of X-Man mini's.
I mean, maybe Uncanny X-Men will be the seventh series running alongside the Age of X-Man titles in having Wolverine, Cyclops, and a myriad of remaining X-Men trying to resolve the fallout from Dissasembled. I mean, it'd be pretty neat seeing Logan & Scott working with Alex, Emma, Sean, Warren, Illyana & Raven as an example.