I am having a similar issue with the Yakima 16 skybox. Currently have two LFD crossbars and the new LFD crossbar with integrated wind fairing. The wrap around clamps of the Yakima will not fit between th3 first crossbar with the wind fairing and the second crossbar, given that they need to be pushed all the way to the front to allow the hatch to fully open. I was hoping the Thule Force XT L would work, with the slimmer clamp design, however from your post it seems the XL model has the same problem as the yakima. Any idea if the L model would work, it is a bit shorter.
I somewhat prefer the thule force boxes because they have metal rails, which give them a 40 lbs capacity increase over the yakima, which is all plastic. The problem is, can you really use the full 165 lb capacity of rhe thule box? 165 plus 40 lbs for the box weight, plus another 15 lbs for the LFD bars technically exceeds the capacity of the stock roof rails.
Another reason I prefer the thule box is that it is thinner. The yakima box takes up almost all of the span of the LFD bars, which are quite short in comparison to other rood racks, at 40 inches. I could probably fit a plano box/kayak mount/gas can next to the thule box, but not the yakima.
Finally, i have considered getting a 3/4 roof rack. However, I have not found a roof rack that works with the Thule Force box, because of its front lip. It seems tbe Yakima is a better fit for roof racks, although it is wider and leaves less space for other uses. The LFD roof rack is nice, but again, is kinda narrow.
Appreciate any ideas here. Have I missed any options?