I agree. The back of the trunk is metal, and even if you drilled holes in it, you have about 2-3' of engine which is all metal, then the cabin firewall, that has about an 1' of padding to muffle the engine noise.
I don't doubt that your hearing something, but I don't think you're hearing the speakers. Maybe the vibration are moving some thing in the cabin and that is amplifying the sound, or something.
Also, where you driving with the top up or down? Slow or fast? When you managed to smell the burgers in your trunk, and when you hear the subs.
