I thought I may have had a pic of the boot install of my KE25, prior to parting it out.
It had two panels on either side in the boot and behind one was the amp, the sub could be mounted on the opposite side, which would indeed retain the access to your spare wheel.
If you had time and welding skills, you could cut out the spare wheel well, weld in a flat sheet of metal and do a boot install and mount the spare wheel up under the car as seen on the KE3x panel vans with the appropriate carrier bolted up underneath.
That way you would still have access to your spare ;)