Nobody has got this quite right yet, and for good reason. You'd have to have been reading a lot of different comics to get what's going on here.
In Spider-Men, a rift was opened between the 616 and 1610 that allowed (616) Peter Parker and Miles Morales to meet and have an adventure. Since then, this portal never actually closed entirely. In the period since Spider-Men, Tony and Amadeus Cho from the Ultimate Universe have been studying this rift. And it's in the pages of All-New X-Men, during that teams recent journey into the 1610, that we see this rift close right in front of Tony and Amadeus.
This story is based on an alternate timeline in which the portal did not close but actually exploded, merging the 616 and 1610. This is why we see a version of the scene from All-New X-Men play out in Ultimate End. And since this is set in a period just before AXIS, it's why 616 (616-A?) Tony in his normal armor and not his recent iArmor design.
In addition, this story is set on the Battleworld version of Manhattan from the start. Essentially, we're supposed to accept that there was once a 1610 and 616-flavored Battleworld: Manhattan (as this is how all the denizens of Battleworld believe the universe and planet to have always been). It was during the rift explosion that these two merged to form this current version of Battleworld: Manhattan. No incursions happened in this universe. It's simply been as it always has.
This is why Spider-Man is there. This is why Hulk and 616(A) Tony is there. And why even Scott Summers is there (sans Phoenix).