How about this - a combined sub box/storage bin? Make a part of it the sub box, and lay a metal plate in between layers of fibreglas to protect the back of the sub - it need not be much - just a reinforcement of the fiblreglas.
The box could be built to fill the rear area, the sub can be behind a grille (or other protection,) facing up and slightly forward. While it's true that bass is non-directional, for a "clean sheet" build, why not point it forward anyhow?
No need to make it too tall - perhaps a little lower than the seat back. Allow some ventilation on the sub side, and we could tuck the amp in the box as well.
Storage can be accessed by a "bin" lid (probably best and easiest) or a drawer on bottom sliders (I'd not trust the sides too much, unless they are reinforced. Loading the wrong way...) The personal option of adding some sort of "storage forms" for custom purposes would work well also, methinks.
Having the "bin lid" open from the rear would also work - and prevent the need to remove everything from the top of the box to get into it (I carry two jerries, a 6.5-gal literjon for water, my first aid kit, a large ammo can with road gear, ...)
Just rambling. Oh - Dew, did I ever get gage measurements to you for that "eyebrow" idea I ran past you? Or do you still need them?
5-90