The whole shyt is going to suck, but being that it's already dumb that Venom has been roaming free in the Spider-verse unchecked by any version of Spider-man, they'll probably just do some alternate dimension shyt where they can have the actual Mary Jane and more comic book accurate versions of the characters, Peter included. Into the spiderverse had a female Doc Ock and all kinda wild shyt that worked great in animation. But as I said, the mediums don't often translate very well...DC has GREAT animated films.
Their best bet IMO is to try and do a live action into the spider-verse where nothing really has to make sense and hope the mediums can translate well and people can get beyond the clusterfukkkery of it all.
Good luck
Those MCU Spider-man movies don't count toward Sony's retention of Spider-man rights. Anything they try to use from them will probably be grounds for legal action for creating false association, which is probably why they pulled the Tom Holand cameo from Venom.
For instance...there is no Michelle Jones that originates from Spider-man comics, she is unique to the MCU. The closest thing resembling her in the comics is a college student that becomes one of the Inhumans in an Ironheart storyline...if they really gonna reboot Inhumans and possibly do a live action Ironheart, they could put her in it or just make her Ironheart. Would make more sense than Shuri or some random MIT student.