I'm not far enough along on my build yet to try it, but I'm leaning toward using Yakima Tracks along the roof which can then take Yakima towers and use normal Yakima attachments. It would also allow some forward/aft adjustment. Because of Yakima's round bars (compared to Thule square bars) I won't have to worry about the curve of the roof causing the bars to be tilted compared to one another. I have many Yakima rack parts and bars, so I could reuse what I have.
See
http://www.rei.com/search?search=yakima%20tracks These come in different lengths and with or without their Plusnuts. These are also available at etrialer.com and other places that sell Yakima. It uses Control Towers and their Landing Pads (#1, since other #s are for certain factory racks).
I had these tracks on a minivan about 15 years ago and they worked really well with no problems. Since a van roof construction is different from these trailers, we'd need to have some minimum support and proper fasteners. The thing I am not yet sure of yet is how much the Tracks can be curved to match the shape of the roof. I was thinking of going to a store and see.

These Tracks would have the advantage of having a low profile when not being used. Another approach would be to just fasten down the Landing Pad #1 in 4 places but it wouldn't be adjustable like on the Tracks.