During the warmer months, I ride with the windows down all the time and there isn't any remarkable noise unless, I only roll the rear two down and none of the others. After having the Sun Roof window track replaced under warranty, it now buffets if that's the only window that is opened. I think this is from wind getting into the headliner area, turning it into a giant subwoofer.
Does pressing on key areas of the headliner or door panels change the noise at all? Does temporarily removing the rear deck change it at all?