As a followup on this I just took a major roadtrip with a full trunk, and the deep resonant sound was completely eliminated. So to summarize:
- The pressure issue and the boominess are separate problems.
- The pressure issue can be fixed with tubing, hatch stop adjustments, and rotation of the bottom hatch stops.
Which leaves the broader problem of deep resonant frequencies. Given that a double layered 12lb. sound blanket over the trunk does very little, though a bit more when placed in the underfloor storage area...I'm inclined to believe that the sound isn't originating from the trunk area, but rather traveling to that area and bouncing around in it. This would explain why no amount of sound proofing measures, butyl installation, etc. anyone has taken have cured the problem.
Now I'm wondering if there's somewhere else in the cabin we can target. For now I feel like sound blanket or similar in the under floor storage area, plus the parcel shelf, is about as good as you're going to get while keeping your trunk mostly usable for daily life.