I would take advantage of the pass-thru opening because you can get some killer bass, and save trunk space at the same time. You can go infinite baffle (lots of info posted on this method here, just do a search), sealed enclosure with the enclosure mounted to a baffle behind the seat and centered so the woofer is firing through opening, or ported, with the enclosure mounted to a baffle but with the port positioned so that it's firing through the opening, and the woofer firing into the back of the seat. The latter is a method I employed in my old Mazda 6 (see attached photo) and the results were spectacular. In each case I recommend you seal off the trunk from the cabin to keep the front and rear waves apart.
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