I kind of have the same issue with the rear being essentially wasted but mine is the 3rd row along with my sub box behind them. Never knowing when I will need the 3rd row I leave the seats back there just folded down. I am in the process of making some kind of fold up platform that will lay over the 3rd row seats along with the sub box in the rear behind the seats. I use the cargo area all the time and need access to it. Not sure when I will actually get started on this little project but with what you have already invested in this truck thus far, an idea like mine may be of help to you. Only thing is that It will be a full fab job as this was for your sub system.
My idea is pretty basic, 3-5 planks of wood hinged between them and anchored by their own weight with notches (think of the factory type cargo mats or cover that you see in hatch back car/suvs). Easily folds and unfolds and is stored in the back between my 3rd row and sub box. I was looking at covering it with vinyl or carpet to match black leather or a type of spray/rolled bed liner since I never know what kinds of things I will be throwing back there, most likely the bed liner but not sure yet. I kind of used the idea of a fold up tonneau cover for the idea
