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I have worked around this problem by
  1. Tagging all objects with a value indicating their intended rank grouping
  2. Selecting sets of objects via that tag value
  3. Using System Events to click the "Same" radio button
This achieves assigning the shapes to their proper rank groupings, still using entirely Applescript.

However, the next problem comes when I ask the canvas to do the Layout. If I first select the "Minimize Crossings" mode, the applications locks up, consuming 100% of the processor, and never performs the layout. I am leaping to the conclusion that it is hitting an infinite loop in the layout code caused by some conflicting constraints due to the object ranks.