I guess I'm in the minority here, but I didn't find it senseless. These are "reborn" 616/1610 guys, which explains why they don't remember anything from the Incursions and might be an in-story way to address why their SQs don't line up (Pretty sure Bendis just wanted regular 616 Tony to fit the character interplay he planned, though
); there are no alternate universes left, yeah, but couldn't there be pocket "dimensions"/planes of existence within the Battleworld domains that weren't accesible by regular means? After all, the extradimensional realms of demons and stuff like that was still considered part of their respective universes, not alternate realities altogether, so it's coincevable that Doom rebuilt some manner of dimensional structures.
There are a number of problems with the issue otherwise, though, namely the fact that it could've been just a #0 issue considering how nothing beyond the initial situation was established, and even that was sort of addressed too quickly. I suppose it will have to be uncovered as SW goes on so as not to spoil things that are crucial to the main book.