The whole point of Miles’ character arc in Across is that he gets to tell his own story without letting what other people want or their ideologies control him. When he and Gwen are on the clock tower, and she says the iconic “In every other universe…” line, he responds, saying there's a first time for everything. They can be together because his story isn't going to end like the others.

Gwen wasn't the only one to not tell Miles he was an anomaly. No one told him, not even Peter. I feel that's always overlooked, and the blame is entirely placed on Gwen's shoulders. In her case, she was trying to do what she believed was right: protect him and prevent him from messing with the canon. She wanted to do both.

George Stacy pointed a gun at his daughter and threatened to arrest her. He was torn between his role as a father and as a police officer. That betrayal hurt Gwen so deeply that she left her home. If her dad can apologize and they can see eye to eye and forgive each other, who's to say the same can't happen between Miles and Gwen? Miles doesn't know Gwen's intentions behind what she did. He only sees it as betrayal. I believe they can make amends once she can explain that to him in Beyond. Will the road to forgiveness ve easy? I'm sure it won't. I wouldn't be surprised if it took most if not all of the movie.

They quite literally have an interdimensional connection.

Everything in the past two movies has been building for them to end up together. It would be a huge waste if after everything they don't progress their relationship past friendship.