That is better then the Toyota Prius, which makes a pulsating "thud, thud, thud" throughout the cabin.
Any vehicle design is vulnerable to harmonic flaws at some point.

^ The "thud thud" must come from the rear windows, correct?

Yessir. Feels like it's trying to pop out the rear window or eardrums.

How is the window to frame fit? You should be able to shut a piece of paper in the door between the window and weatherstrip, then not be able to slide the paper out. I believe the the window adjustment is the same as the 996, there are two plugs on the underside of the door that reveal two nuts mounted from below. You loosen the nuts and move the bottom of the window regulator track to adjust the window fit. Track moves out to move the top of the window in, vice versa.