I concur that the noise was really noticeable the first time it rained. Quite bizarre if you tell me as if the hatch was open.
But recently I have not notice much sound back there even when it rains. I don't know if I became accustomed to it or what not because I always wanted to Dynamat it but never got to it. Then I realized that it was not that noticeable much.
It may be because of the following:
1) I bought a cargo floor mat protector made of tough plastic that covers the whole area. (heard the cargo protector works too)
2) I placed some type of garage absorbing mat in the back. (double size of a usual welcome mat)
3) I placed this black soft cushion for large dogs in the back to protect the area even more so I can throw junk in the back.
4) On top of that I placed some extra floor mats I had lying around as another layer of protection for the heck of it.
5) I once went to the post office and placed some priority boxes not folded yet for future use under the cargo mat. Hence any cardboard for that matter works. Is another layer to deaden sound.
6)Play a little music helps but no need to blast it.
All this was really to protect the cargo area from junk I throw in the back but it seems to quiet the noise there alot. Moreover, it still looks like a flat area and not a mound of mess either. Just use your imagination to muffle the sound and it should work too.
All this has really muffled the sound of rain to practically nothing for me at least. You can also try putting a blanket in the spare tire area.
These are quick ways to decrease sound.