Alright, so I realize that it keeps being officially stated that Spider-Man: Freshman Year takes place in the MCU. I don't usually like to speculate, but in order for this to be the case based on the clearly altered history we've been seeing, that only leaves one option.
The comic storyline where Peter's history was altered via magic. Like in No Way Home! It's called Spider-Man: One Moment in Time. After One More Day, when Mephisto exploded Peter and MJ's marriage, they had to fill in the stretch of time that spanned, you know, decades where the two were a happy couple.
Now it's been a few years since I read it but I remember Spider-Man getting into it with a thief, falling off of a roof and getting knocked out, causing him to miss the wedding. Then one thing led to another and Peter and MJ broke up. Thus, no one remembers anything about Peter and MJ ever being married, because they never were.
So, if no one in the MCU remembers Peter Parker, what do they remember in his place? What happened that altered the timeline and made it so that Peter was never a part of their lives? So that he never met the Avengers, or befriended Ned, or started dating MJ? Spider-Man: Freshman Year is probably telling that story. As Uatu says, one decision can shape an entire universe.
I hope this clears up all the confusion! I might be dead wrong, but it's my best guess, and makes the most sense. Until next time, Face Front True Believers, and I'll see you in the Multiverse!