It’s impossible to help you unless you post a link (or attach) the bom plugin you are using.
From what you wrote here so far I can not tell if kicad_netlist_reader.py even has anything to do with it at all.
Also consider using pre-made bom plugins that are quite powerful in terms of various output capabilities and already handle things like skipping virtual components.
See user plugins list at the bottom of the post here: