I would argue that the preconceptions coming into a season affect the perception whether it's supposed to or not. If Wilson is perceived as a top QB heading into the season and then has the best season, what argument can stand against that?
Let's say the positions were swapped with Allen having Wilson's numbers (the best) and Wilson having Allen's (2nd or 3rd best, depending on how you break it down - but very close).
I'd say, Wilson would still be the favorite owing to his track record. Unless Allen is clearly head and shoulders above the competition in production, like Jackson last year and Mahomes the prior year.