A speaker creates sound by pushing air at different frequencies. What you hear are the sound waves from that air being pushed. Now with subs in a sealed trunk with no direct passage into the cabin how on Earth could you hear the air that is being pushed?
It's thus questionable to state that the bass "punches right through" as if somehow magically the air jumps out of the trunk and into the cabin. Just because bass is omni-directional does not mean that it's omni-present too.
What you're hearing is the thump of the bass hitting your trunk and you're definitely FEELING the vibrations in the car (which probably has more impact than anything).
If you're happy with it though and think it produces a good, clean, tight bass, then that's all that really matters. Enjoy.... When I worked for Harman on their OEM sound systems we also would install subs in the trunk (for factory upgraded stereos). It wasn't ideal but was usually the best we could do with the packaging options that we had. I think you've probably done the same here.