I mounted an old Thule ski box on my 2009 Outback and it blocked the hatch door from opening. The only way to correct this was to drill new mounting holes farther back in the ski box to allow mounting it farther forward on the Outback. Now it overhangs the windshield and I'm not too confident that it is a safe mount. It is as far back as possible while just clearing the open hatch.
If you are using a ski box that does not block the hatch from opening fully what make and model box is it? If you, too, modified your ski box to make it fit how did you do it?
What you need is the new Packasport 71SS. It is designed specifically for the wagons and cross-over suv. You will be able to open the rear hatch without hitting and it won't stick out over the windshield. Check us out at packasport.com