They alluded to The Commuter Commuteth in the last movie and that's a fill-in during Defalco's run. I also think they are going to allude to Parallel Lives, since they implied she knew a lot about Peter in the first movie, and that's how they'll bring in Uncle Ben's death in this continuity. That's a secret Peter hasn't told Ned Leeds, Tony Stark, May, but she will know. Of course the impact of parallel lives is diluted since so many people know his identity when originally MJ was the first member of Peter's long-running supporting cast to find out, and of course Bendis' Ultimate equivalent of that (USM #13) doesn't work because Ultimate MJ's role as his sidekick/confidant is given to Ganke Ned.
The idea and hope I guess with these Sony-Marvel MCU movies is that slowly they're going to make their short-notice quickly patched-in continuity Spider-Man become the traditional and classic take on the character and setting, and do it in a way that makes it fresh and avoids Raimi-nostalgia. So the idea was to introduce Michelle Jones as a kinda-sorta-maybe-couldbe version of MJ in Homecoming before making a commitment.I think if they had intended her to be more overtly Mary Jane they probably would have gone with a depiction that was more in-line with what people expect or usually imagine the character as.