Mine definitely doesn't have the spring loaded stops. Mine have a silver nut which you unscrew then rotate the rubber stops.

I've gone through my trunk and tightened everything but the noise is still present :(

Have you checked that the folding seats are locked into place?

Oh, and IIRC you posted about aftermarket sub enclosures? If you have an aftermarket enclosure it could be that or related to that.

Do a process of elimination procedure. Put the seats in the down position and see if the noise persists. If the noise is still there begin by removing the aftermarket sub, then go for a ride and see if the noise exist. Then remove the spare tire components, go for a ride and see if rattle is still there. By now you get the picture with the process. Chances are something was not affixed back properly when the PO did and upgrade. You should also take a look at the area were the radio/NAV/CD equipment is 9/10 a PO may have augmented the rack system to accommodate an aftermarket amp for the sub or some other modification and did not put all the screws and nuts back in.