What you describe was a thing way before Slott and well before OMD. Anytime there has been any major change in Spider-Man be it a costume, career, romance or membership of a superhero team it's never too long before the status quo is back. That's a bit of an issue I have with this book; while there some nice character work the book looks like it's trying to write a cheque that Spencer will never be able to cash. Peter going all meta and realising that no matter what major changes happen in his life he always ends up single, broke, loner superhero working at the Bugle. Even if Spencer does undo the Mephisto deal none of that is going to change. One More Day was a symptom of this problem not the cause.
I don't really see what erasing the OMD continuity will do. More people liked those runs than you think and once again it would be futzing with history. You can undo OMD without erasing what went before. I didn't read the Mary Jane series so I missed why she is working with Mysterio but it seems bad that she seems to know a lot about what is going on with the metaphysical forces manipulating Peter which seems at odds with her in being in love with him. I wonder if at the end of this the Mephisto is null and void only for Peter to reject MJ for not being honest with him.