I was just about to try to figure this out too! I'm having the rattle from the rear deck where the subwoofer is.
I verified the rattle goes away temporarily using two tests: 1) I press down on the speaker/grill assembly, or 2) open trunk and push upward on the speaker or metal deck.
So I think there is just a gap between the upper speaker grill parts, and the underlying metal decking. I'm going to see about bolting them together snugly, and if that is not practical, then I'll put something between them to absorb the vibration against each other.