That vibration when the moonroof is open is a pressure differential from inside and outside the cabin, I think. Does it happen around 30-35mph? And it kinda sounds like a helicopter flying overhead? I have that whup-whup-whup sound too, when my sunroof in my jeep is open all the way. It also happens when I have the rear windows open symetrically.

Crack one window when you have that roof open and see if it goes away. You'll be equallizing the pressure.