Just the other day, I developed a bit of a creaking/popping sound (not quite a thunk, yet?) that's coming from my the cargo cover crossmember on the passenger side; I'm at just over 5k mi. Since I'm betting it's structural to some non-critical degree, I'd say it could very well be louder (via propagation) if some of your rear cargo area paneling has been removed. I'm betting since you've already got the rear cleared out that the cargo cover's also been removed, but on the chance it's not, maybe give it a whirl without and see if the sound is still there.