When I finally get to mounting some lights on the rack I'm going to route the wire through the headliner then out through one of the stock locations in the corners of the body at the upper part of the hatch.
the best options (IMO) include the use of marine-grade rubber grommets to send wire thru- the roof with no shaffing on the wire, and more inportantly, a water-proof seal/connection
i ran my wire from the rack right down betweeen the drivers door and the rear drivers side door. i used plenty of silicone to seal it up. it is real tight against the roof and doors so it doesnt get ripped off by branches and other things... i can have some pics in day or two...