Assuming you could clock it correctly, you could get a length of 1" square tube* (length determined by mounting flange in chosen kit), drill and tap a 1" square cap plate to match the 1/2 x 20 bolt, then weld the cap to the tube. The tube will then thread on the bolt (again, needs to be clocked).....this would replace the mounting flange in either the Yakima or Thule rack kits, providing a square stock stub for the rack. I suspect a drilled and tapped plate would be need to receiver the rack lock and tightening knob as well. I can sketch it up if that doesn't translate...
* 1" is the size of the tube for my Thule, I'm assuming it's the same for the Yakima but can be adjusted to suit chosen rack.
Forget all of that...I think the Thule mount might work with your setup as is....check this photo of the back side (front of vehicle) of item B, the mounting flange...
That bore in the center is ~ 3/4" in diameter, it should clear your bolt. If you think it might work, I can send you my flange to test fit before buying anything.
