Sure, it’s possible. Select both VTP models in the Pipeline Browser and add a Python Calculator filter. Set the expression to inputs[0].Points - inputs[1].Points. Click the Python Calculator filter, then select the File -> Save Data… menu item and export the result to a CSV file.
As of ParaView 5.5 (maybe 5.6?), the order in which you select the pipeline object is the order in which they are arranged in the array. It’s not ordered by the arrangement in the Pipeline Browser.