Some updated info for this thread. I went down to the dealer parts department and asked them the question about the mounting points. The thread size on the Cross' roof rack mounting holes is 8mm (metric). The Thule rack uses a set of four proprietary feet (they call a Fixpoint mount kit) that is sold separately from the racks for $150 USD. These attach to the Cross roof rail mounts using four metal studs with the 8mm threads. The rack crossbars then attach to the Fixpoint mounting feet.
It appears that the 8mm studs are the sole load-bearing members of the attachment points. The Fixpoint mounts don't appear to use any other bracing or tabs that attach to the Cross' mounting points. In fact, the Thule Fixpoint kit includes plastic replacement covers for the plain Toyota covers that fit overtop of the rectangular mount space, the only difference from the stock covers being a small hole for the 8mm stud to pass through. The Thule feet then attach to the stud on top of this cover.
I still don't have any info on the Toyota racks in terms of how they are attached. It's still an unknown why they have such a lower weight limit than the Thule racks. If I had to guess, the studs are probably not the weak point in the OEM racks, it's probably the crossbars themselves.