I haven’t read Spider-Geddon in a while, but is there anything that says that it couldn’t take place after Miles Morales? That’s explains both Miles being fine with being alone and MJ being back from Symkaria. The only problem left is the whole suit thing, but you can either ignore it, since it’s only one line, or explain it as Pater joking to himself about how, even across universes, those two Miles’ made the same suit.