Originally Posted by rob_rector
..reason I bought my Compass was because I could put my bike inside ..
Same here. I actually brought my full suspension mountain bike to the dealer and made sure that it would fit inside (If it fits then all my other bikes will fit).
The way the roof rails are designed precludes the use of any aftermarket roof rack system and since you have the ralley body kit a hitch mount may be out of the question. So, by default the Mopar roof rack is probably the best bet.
If I need to transport more than one bike then I just use my Father's Liberty on which I put a couple of Thule V2 mounts plus it has a receiver hitch if I need to carry more than two bikes.