I have managed to get two 3-1/8" deep odyssey batteries under the rear left seat without mods. For some reason, the floor under this side is shaped differently than the left side - more space/depth. Even by cutting out the floor and building a box that sticks down below the existing floor you might only gain another 1-1/2" to 2". That would leave around 5" of height to work with (unless you start modifying the bottom of the seat itself). Can you find an optima that short? Perhaps odyssey has some higher rated batteries that would fit.
Also, would you be affecting the structural integrity of this already soft floor system? The mounting point for the rear subframe is right there under the seat.