Another reason for things in the backstory to change would be the sliding timescale. 2099 was originally over 100 years in the future, now it's only 83. And some of the 2099 tech now exists in the present day even without Miguel's involvement. For example, Lyra. Her tech would simply be an updated version of Tony Stark's AIs. Functionally, there's no real difference between Lyra and Friday.
Various time travel incidents, such as the O5 X-Men's arrival, would also alter the future. That particular incident has already averted Old Man Logan's future. Logically, it would affect Miguel's as well.