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I have the rhino rack low mount. I've opened the sunroof with the bars attached but not the cargo box. There isn't much extra clearance so I don't think you'd be able to with the clamp on it.
Just found another option. I had a set of RhinoRack Vortex cross bars from a previous vehicle. They now list on their page a set-up similar to the Yakima, but about $150 cheaper if you have to get the whole package. I already have the bars, so I only need to buy the base kit and legs. Ordering...