The docs for PrimSpec mention a mutable .variantSets attribute. Calling del primSpec.variantSets[variantName] removes the variant set definition but there are still entries in the “prepend variantSets” and “variantSets” metadata tags. Not sure if this is an issue on the Nvidia or Pixar side and whether anything can be done about it without manual editing.
The command you may be looking for is primSpec.variantSetsNameList
That should allow you to modify that actual variantSets ListEditor
Hope this helps!