I would think most casual Spider-Man fans these days would think MJ knows Miles (based off of the PS4 game).
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Now I want a flashback story where a beat up Miles shows up at Peter's apartment and MJ provides some first aid.
Miles' origin in 616 (if that's what they're going for these days) would put him post-OMD, and pre-Spencer.
So, you know, it's funny that MJ knows.
Nor should he tell people that. Peter should keep his home-life to himself and people who are much closer to him than Miles and Spider-Gwen. They're on good terms with him, but there's no need for them to be involved in Peter's personal life, just Spider-Man's hero life.