Exactly! Doom would never just create a few characters for shitts and giggles. Ultimate End is a special case and as Bendis has said, it will get explained (hopefully) in due time.
As for Spiderverse, thats another special case. Spidersense is making them aware that something is wrong and thier memories are muddled but it doesnt outright mean they are 616 versions. Only that doom messed with memories, which he has done to everyone on Battleworld to hide the true 8 year timeline.
Everyone Dies! Except Doom, Strange and the life raft survivors. Thats the whole point of the story.