The burden/stigma he will carry with him on draft day, and once he's on a team, is the air raid offense he came from. I suspect if you went back and looked at the film of Goff, RG3, Geno, Johnny Football, and even Brandon Weeden you'd also see some similar throws and reads. There are GMs that probably have very strong opinions on guys that come out of that system. Like not on the board in any round kind of opinions.
No one that has come from that system has had anymore than one season of success - RG3 and, of all people, Nick Foles. The rest make the Bills QBs since 2000 look like Pro Bowlers.
Can Mahomes buck the trend? Maybe. But if you were a bettor, and GMs in a way are betting on players, would you really expect that he's the one guy out of that system that will end up being a franchise or even an above average guy in the NFL? Doubtful.