I like what you've done. My design idea was similar when I started but I chose to go with a large plastic cargo box such as is found in trucks. I dropped all of my odd shape spares and tools in it like shovel, bead breaker, spare driveshaft, come-along, rope, air hose, etc. Everything that was long or not conducive to being stored in a tool bag. The box is sitting on a platform where the rear seat used to be and serves a similar purpose to yours in keeping weight low and in one place.
All of the tools and small spares went into bags to keep them well separated and quiet on the floor in the rear passenger foot wells keeping the COG as low as possible. As mentioned, the potential for noise would (did) make me crazy. The benefit of bags is being able to get the size down to something closer to the actual space that is required, not leaving extra space like a fixed size box does. But this is an area of personal preference and like all things will be tweaked as time goes on.
As for your spare, try finding a YJ adjustable spare mount and bolt it to the floor. This gets rid of the tie down strap and gives you back the nooks and crannies the straps steal from you.
Nice project.