I am posting this in case someone in the future may have the same problem. I searched for the source of this rattle/clunk for months with no luck.
I had a rattle/clunking noise that sounded like it was coming from inside the rear of the car around the back seats. It only happened on rough roads or when going over uneven pavement such as driving up onto my driveway or going over potholes.
It turns out the trunk itself was moving when the car flexed. There are adjustment bolts on each trunk hinge that are supposed to support the forward part of the trunk. The bolts on my 2021 M3 were run completely in. You could push down on each side of the forward trunk and get it to move. I slowly adjusted the bolt heads outward and repeatedly closed the trunk to make sure I was not going too far. I couldn't find any documentation on proper trunk hinge adjustment but I made sure the trunk was not preloaded on the hinge.
I have attached pictures to help.
This noise drove me crazy for a while and Tesla service couldn’t find it. It would be nice if the moderators pinned a thread for confirmed rattle and noise fixes.