I had a very similar issue. It was the heat shield between the muffler and the trunk bottom. I noticed it when I tossed something in the trunk and it made the rattle. Pound decent on the rear trunk bottom and see if it makes your sound. Only really did it when warm. Just pushing on the shield bent it enough to stop the rattle.
'04 Boxster S 50 Jarhe 550 Spyder Special Edition 851 of 1953 made, 3.2L, 6-speed manual short-throw
'Cause you know the Germans make good stuff!!