How about a stand alone unit like the Infinity Basslink? I had one of those in the TJ that fit perfect behind the backseat. I used a breathable fabric that repelled water and laid it over the Basslink and bungied it at the base. Aside from having to use an air hose to blow out the dust once a year, it stayed pretty clean. It still got a little wet, like when I washed the Jeep ans sprayed everything out, but overall it held up well.
2013 JKU Sport, billet, auto, 3.73, LSD, 315/75/16 Duratracs on MB 72, 10A springs, Bushwacker flatties
Sold - 2005 TJ, red, auto, 3.73, 33" Duratracs, 4" lift
Ice storm casualty in 2007 - 2003 TJ, green, auto, 3.73, 33" Duratracs, 4" lift