I think back to quarterbacks such as Bernie Kosar with his funky side armed delivery. He won a championship. Think back to Frost who always looked like he was still throwing the shot put. He won a title. Young at Texas wasn't Joe Namath, yet he won a championship. It's about running an offense that suits the quarterback. Not full scale changing of the offense, but leaning on the plays and schemes within your offense that's plays on your quarterbacks strengths. Martinez still has two seasons to refine and polish his game. He wasn't done any favors by the coaches changing yearly as well as the playbook. Payton Manning never won a national title. He was beat by an option quarterback as I recall that had an only fair passing percentage. But what that quarterback did, he did very well.
The list of "unconventional throwers" is endless...Tebow did alright too.
You are exactly right, the QB is 1/11th of the offensive attack. A central 1/11th, but without the supporting cast, he's limited.
Many qb's don't flourish until their 2nd or 3rd year running the same offense.