The Yakima Skybox is 10" longer than the Thule. Does it sit higher than the antenna or did you just bend the antenna?
I was able and have the box mounted with the stock antenna. However, if you dont want to have the box touch the antenna it sits a little farther forward than it should, you can see the overhang in the picture. The result is a lot of wind going under and pushing up and the box moves around a lot more on the highway, plus youre not maximizing the distribution of weight very well. If I want to maximize the distribution of the box and put it as far back as possible without hitting the hatch the antenna gets bent over (what I am doing now). Not a big deal since its rubber but just seems like it cant be good for the antenna long term.