the side bars on my rack would be pretty close to the body, like shran mentioned, exo cages get hung up on shit. i think you would need the lower horizontal bar to add to the rigidity (did i make that word up?) of the whole thing. you could also make the bars that come down the side removable. put them on when you wheel and take them off when it goes back to DD. use cotter pins or something to keep them together. my exploder is my DD, so i'd just attach mine permanently.
i'm just gonna be careful with my b2, if i break one, i dont know what i'll do. i bet a new window would leak (or maybe just fall out while i'm driving down the road) i'd probably chop the top and figure out a way to make a camper shell fit.
i think the plexi glass route could work too....it would just take some thinking and testing. doubt it would be waterproof though.
why not find a way to make the glass removable? have some kind of lip that it slides in and out of that you could tighten down as well.