I would do what your thinking about for sure. Then I would look for plastic boxes (Look on Amazon - type in the size you need) that fit in that space. Get some tall and some short boxes that you can double stack them. Just an idea.
Hopefully someone has a simular setup that can offer suggestions.
2017 Axis / 25.4: Big Foot Levelers, Aims 1200 Watt inverter, Ceramic Window Tint, Full River AGM 6V batteries, Front Hellwig Sway bar / Rear Track Arm, Safe T Plus Steering Stabilizer, PD 4655 converter, Hard Wired Surge Guard, WEboost + WiFi Ranger, LED Headlights/Driving lights, TPMS, Surge tank, Tornado flush, Viair Compressor