If you are back farther, that is farther you are throwing the ball, more time for the defense to react, too. Also, a deep shotgun gives you an easy angle at defensive end, or whoever is coming off the edge to rush. Has to be harder to snap that deep too, so why not have someone coming hard right up the gut?
My only question is do the ref's extend their idea of the "box" that you need to be out of to throw it away when in the shotgun? I wish that rule never made it to college. What will be funny is if we play Mizzou and it turns into a defensive slugfest, everyone will be scratching their heads then.