Its so hard to say. In the SEC all you do is run and his wide open WR's You dont know anything about their true field vision, and D read ability.
I would think a QB from a lesser program from a major conference would have a slight starting advantage in the NFL over a major program in the same conference. You have to do more against quality competition. For example, Brees, Cutler, Rivers, Shaub, Rogers and Eli.
But then again, the top 2 qbs are from major programs at the time, michigan and tenn. They werent passing schools but major programs still.