I have early Jun model and the hole is covered with material but still fair amount of noise that I would say seems to be around doors, as far as I can tell.
Assuming by subwoofer pass through you meant that whole in shelf at back?
Temporarily tape the suspect area with painter's tape and see if the noise diminishes considerable. If it does, you might just had a seal issue - easily fixed.Same. My only complaint about this car. It really sounds like most of it comes from the back side of the front windows. My passenger window is especially loud.