Thanks for all your input!
Before reading your posts on the subject, I noticed my GLA45 was making the thumping sound in the back (after 1800 miles). So, I folded and closed the rear seats a couple of times, each time making sure the seat belts were not stuck between the seats and body (which a bad design to begin with). Also, I played/pushed the spring loaded holders under the trunk shelf to make sure they weren't holding the shelf unevenly. The holders are actually what holds the trunk floor up when you need to access your spare (assuming you have one).
The noise is gone for now but sounds like the real issue is the latch. I just couldn't get any play from the rear seat latches on my car, so will find out soon I am sure
Thanks everyone for the input, i suggest we keep this thread active so future owners can have a reference. For the record the noise initially reported by me is a knocking noise (think a marble dropping on a hard floor, or a door knock with a finger to wood sound) i have felt taped a whole lot of the rear trunk already. Including the pivot points on the rear trunk, the touching points of the tow hook, air pump in the trunk.
The knocking is still present however, will have to look into the latch, although there's no play in the seat in the lock position. I have not felt tape the actual latch just yet.
Kerim, do you mind showing a picture with the exact part they fix/replaced? or a copy of the work order form the dealership would be useful as well (block out your info)