Update: There is truth to some of the other people's anecdotal reports of vinyl tubing not resolving booming noises in their Model Y. I met with user
@BrianZ last weekend, and we did 5/16" OD tubing, calibrated the hatch, with not great results. Put in 3/8" OD tubing, and the gap was too huge (but it seemed to resolve it pretty well), so had to resort back to 5/16". With rigid hatch stops, and vinyl tubing and calibrated hatch stops, it wasn't enough to make a subjective difference. I've done this vinyl tubing install on 5 Model Y's and all had improvements until this one.
The only other items I can recommend in that instance is:
1) The hatch might need a complete re-alignment (I noticed there was some differing gaps at the tail light areas with that Model Y, and the hatch glass had a hump in a section that extended beyond the roof glass). This has resolved a few users' issues in previous pages in this thread, but good luck getting Tesla to do this. You might have to pay a body shop to do this, and would you trust any body shop to know how to correctly align this piece? I guess it depends.
2) Sound deadening on the rear wheel wells, and as discovered by
@azeteg, sound deadening in the rear doors apparently makes a big difference.