Not my specialty so I can't help. I'm sure you could build a small sealed box for a woofer in the ski compartment. It would not take up much trunk space and reality is our trunks are not super useful ... especially toward the rear bulkhead as you can't reach in there easily. My
bimmertech amp (Audiotec Fischer) has pre-amp outs which would allow for an easy amp/sub add without any mods to the factory wiring.
Filippo