I can't imagine that Marvel entered into an agreement with Sony that would allow them ANY chance of damaging the Marvel comic book universe. I'm sure that any references to MCU would have to be approved and that Marvel would take how good the movie is overall into account. The last thing they want is to have a stinker out there that is in MCU. Not every MCU movie has been great, but none of them have been rated "Rotten" (to use one example).
Yeah, but the thing is, imagine they just ignore the issue.
They can mention Spider-Man all they want. He could be a major character (though perhaps never seen or only shown briefly and in costume similar to Batman in Suicide Squad).
So everybody would know they were viewing a film in the
Spider-Man Universe and if they
infer that is also the MCU, that's not Sony's problem.
As long as nobody in the film specifically mentions Iron Man, Hulk etc., they'll be perfectly within their rights, but if they are mentioning Spider-Man (again within their rights) 90% of the audience (who doesn't study these things like we do) will simply assume they are in the same world they've been seeing Tom Holland swinging around in.
Marvel can't force them to display a big statement at the beginning of the film saying: "Warning! This film does not take place in the Marvel Universe - The Avengers, Guardians of the Galaxy, Dr. Strange etc. DO NOT EXIST IN THIS UNIVERSE, so get that out of your head right now."
My wife, for example, knows next to nothing about the technical details of these things, but she has seen Civil War, and she's seen all the Spider-Man films, and she's looking forward to seeing Homecoming. She knows Venom from SM3, so she knows he's connected to Spider-man. I would expect, if I didn't explain it to her, she would likely see Venom and she would be assuming the whole time it was connected to the Spider-Man in homecoming (even if the film didn't specifically tell her that).
In fact, maybe I can experiment, avoid telling her any of this, and see how she does interpret it.

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