It is September. It is a long, arduous season. 3 regular season games in September is not enough to make Allen better than a guy who six months ago went 8 for 8 in an overtime game winning drive and converted a 4th and 1 with his legs in the Super Bowl. With 1 billion people watching or whatever it was.
And for those saying 'it's not about the past, it's about now,' well that would make sense if the past wasn't so heavily weighted in favour of Mahomes. He has the rings, the SB MVPs, the MVPs, an OPOTY, has led the league in categories Allen never has, a better career passer rating, a better career QBR, more passing yards, more passing touchdowns, less interceptions, etc. etc. And they've played roughly the same number of games.
Allen is better at rushing. That's it. But that doesn't make you a better QB. And Mahomes can also run, so it's not even like this is a weakness.