The thumping could be anything. My guess is that it is the RTABs or RSMs. However, it may be the subframe. Too hard to tell with that one sentence. The owner of the car should have had more fuel in the vehicle so the inspector could have tested it correctly.
However, that being said, it seems to be in very good condition. I don't think they found too many issues, other than the thumping noise. But, I would investigate that further. What is the mileage and year of the M3?
Where is the car located?