1) I don't understand your question.
2). VM in VX.2.2 behaves a little better than VX.2.1, but it does not update the properties in the schematic. Why do you care? Just curious.
Note that you can run the PartLister in DxD when a variant is displayed and none of the X-d out parts will be listed in the BOM.
3) Here is my setup for an Integrated Design. I don't know why it would change for a Netlist design:
If you replace the part instead of 'unplacing' the part then the value does get updated to the new value. That would mean generating 'unplaced' versions of your components (maybe generic) if you must change your displayed value.