Well, no, not quite, he was originally from future 616... until they retconned it to not be the future, just a future, same byline they took with Earth X, MC2, etc. Miguel's future now being the ever-shifting future of 616 (which isn't even 616 anymore, it's just the main Marvel reality, kind of the whole point of the fallout of Secret Wars), is actually back in line with the original 2099 imprint's intentions.
My read is: given how well Secret Wars 2099 works as a follow-up to the end of PAD's original run, with issue 44, we can just view that as the continuation of the original run, with the fallout of Secret Wars/Age of Ultron/Timestorm/any other given Time Travel Event pulling the 2099 equivalent of One-More-Day, which is why when we see Miguel in Superior, it's clearly the same Miguel, he refers back to events from the original run in Superior and v2/v3, just, like, his identity is secret again (well, actually, I'm not sure it is. It becomes clear that Tyler still knows who he is, they just seem to be putting up a charade in front of others), and he's not in charge of Alchemex and is back to just being an employee. But, like, Roberta and Sonny and such are still around, Tyler's not crippled and in a chair (unless you read him in that chair thing in Superior as him still recovering but better)....
Actually, wait, revising my timeline opinions.
I am now going to just say that Spider-Man 2099 stories happen in order, as published.
The Captain Marvel storyline falls sometime after Tyler Stone gets better, if he was even as seriously injured as he was making out.
In Timestorm, we learn that Lyla's fucking with time/travel due to her messed up obsession with Miguel again, and that Doom has been holding the future together through sheer force of will. While the events of the timestorm resolve themselves, some... alterations have occured. Thus, we get Kron-as-Scorpion in Shattered Dimensions and Edge of Time, which, again, time-travel stuff messing things up.
We then rejoin Miguel in the pages of Superior, where he's not the boss anymore, and it's fuzzy on whether Tyler and Miguel openly know that each other knowns the secret identity thing. Either way, he strands Miguel in the past. After several more time/dimension travel storylines, we get an entire background arc about Miguel trying to lock his future in place, and experiencing various slightly-different ones every time he tries to go home, until he finally manages it (the end of Spider-Man 2099 v2 and the entirety of v3, with a brief interlude in Secret Wars, where, again, future gets adjusted a little bit, introducing the Alchamex Avengers and The Defenders).
Hell, if there's no major contradictions, I'm just going to take it as read that the events of LEGO Marvel Superheroes 2 is what chronologically happens next for our beloved futuristic wallcrawler & company.