One thing to keep in mind is to make all your measurements of your trunk space before diving in. I had all these ideas in my head and on "napkins" only to find that most of it wouldn't work because the space is a lot smaller than you think.
My idea was to have it flush with the back of the seats when folded forward to make a nice flat storage surface, I can't remember the measurements, but I think it was only 9" in height give or take an inch. If I got what you described pictured in my head right, you may not have much room to do what you want. But I am interested in seeing a sketch of your design.