Could it be the bearings on the driveshaft? They might be worn just enough to not stop the driveshaft immediately.
I had a similar problem, but I don’t know if this applies to Jeeps. My spare tire was not secured and would shift when I stopped. Junk in the trunk would also cause this (?)
Gastank for sure … mine have been making the clunk for years …
Our 4Runner had the exact same problem. It was where the rear driveshaft telescopes on itself. It was binding during stops and starts. A little grease in the zerk fitting, problem solved.
One day a guy came to my shop, he had the same problem. He bought the car about 2 months before. He told me that he had taken the car to a dealer and 3 inde shops. Know one could find the what was making the noise. I took him for a drive. I would hit the brakes and 2-3 seconds then clunk. I did this a few times and back to the shop. When I got back to the shop I took out the rear seat bottom and removed the pop bottle. Know more noise. My guess is something is rolling around in his Jeep.