Have you guys seen the new generation of 6.5 subwoofers that they are coming out with? They have thick surrounds and 1' Xmax & can hit true subwoofer frequencies
If you did a cutout or infinite baffle into the trunk, I believe a 6.5 might fit perfectly in the armrest hole. Since it only needs .15 cubic feet for a sealed box, I wonder if there is enough space if you gut the under seat sub & plastic enclosure in favor of a fiberglass molded box that still allows for the seat components to clear the subs' surround.
If you are not familiar with these 6.5 subs here is Sundown's version