There are lots of cars with subs in the trunk and also lots of people put subs in the trunk. The thing is low frequencies are omni-directional, or more so than higher frequencies. The wavelength of a 60hz tone is very long, so it permeates through most materials. When designing acoustic foam, you need a material the thickness of a quarter of the wavelength of the frequency you are trying to attenuate. A 1k tone is approximately one foot long, so in order to attenuate that frequency, or absorb it within the material, you need about a 3 inch thick panel. Any frequencies above 1k would get absorbed as well. Low frequencies are the hardest to mitigate for soundproofing because their wavelengths are so long, when you get real low they're like 30 feet long. That's why most subs have a phase switch, because depending on where you place a sub you might not actually hear it because the wave is at its zero point where you're sitting. That's also why you can hear one of those boom boom cars a thousand feet away.
This is just what I know from my experience in the audiovisual field of work, so I decided to do a not-so-scientific experiment. I used a three inch piece of Roxul mineral insulation, which is basically what acoustic panels are made of, and did some measurements with the audiotools app on my iphone. Tone settings are flat, volume is somewhere in the middle. I played a sine wave at 60hz, 100 hz, and 200 hz, both with the grill open and with the insulation taped to the underside of the grill. I then played pink noise and captured the covered and uncovered results. The Iphone was placed over the center console.
One thing I learned is that I have some resonant rattles at 60 hz. Another thing I learned is the rear seats have barely any coverage.
I could see that the cabin would feel more "dead" because there are less high frequencies bouncing around in the trunk, but the sub would work fine if the trunk was completely enclosed. It might honestly improve bass response because sound is pressure, and you'd be increasing the pressure in the trunk when sound is moved through it.
If you are talking about the rear seats, I could see more attenuation of the sound because there doesn't seem to be any woofers in the door speakers, but from the front seats I noticed no change in bass response and the results back that up. So I think covering that grill would be a great way to get rid of some road noise, but probably not the droning type at lower frequencies.
The phase switch on a sub is usually there to match your speakers, which could be on the opposite phase.
Can happen with mixed brands in which subs often are different from the mains.
I agree the foam is probably attenuating some higher frequency noise more than anything.
But the music seems somewhat less punchier in the lower frequencies. How low I don't know.
How high the rear sub covers I also don't know.
Speakers move air and I significantly change the path air moves from trunk to cabin. Period.