I got the factory roof rack installed and put on my Thule box, and was dismayed to find that the rear hatch wouldn't open. It was a bit of a shocking discovery for a 4WD vehicle.
Fortunately, my wife's engineer father Ralph had a great idea once I had dug into the issue. The front bar of the rack is the limiting factor, so we made and added these extensions from
The bolts & washers are all stainless steel from Canadian tire. The ones you can't see are about 1" diameter inside the channels of the rack.
I hope this helps you or others to be able to use your ski boxes more effectively too.
The end result:
The end result: