I can create almost an "air hammer" effect in the CARDIS. Very powerful, very low frequency (maybe subsonic - you almost feel it more than hear it), a few hertz repetition rate. It happens if the back windows are rolled down, the front windows are rolled up, and speed is in the 40s or better. (No, I don't drive that way -- discovered it by accident one day after being parked with all four windows down and forgetting to roll the rear windows up.)
But here's the thing: I never experienced it before I replaced the rear seats with a load floor (and I' ve forgotten the rear windows were down more than once).
I agree it's likely a resonant cavity issue, and my experience hints that INTERIOR changes might also help you. Try some expanded foam or fluffy blankets in the back seat. Not a solution, but it may give you clues to help solve the problem.
Me, I figure it'll come in handy if someone I don't want riding with me insists on "shotgun." Five minutes tops and they'll be begging me to let them out at the next corner.
Let us know what you find out, please; I'm curious.
Cheers,
Rick