Yep. Allen certainly isn't above criticism, but you're right that he doesn't get the credit for doing what he does with so little. Mediocre O-line, never had a great running game, Knox is not close to the top TEs in the league, Davis is an extremely limited number 2 WR, and the rest of the WRs are nothing but journeymen. And yet as you point out he's still right there with the leaders in every category.
I guess a Josh skeptic would say he's the reason Knox and the other WRs aren't better, but I'm inclined to say only Andy Reid could make those guys consistently explosive.