OK, understood on the antivirus. I'm sceptical that contacting Norton will achieve anything though if I'm honest, but I might see if I can find a few other Steam games using nw.js and see if the same thing happens (just to have some ammunition).
There is unfortunately no other "easy trick" for this one. It's the same with certain types of game recording/streaming software not working properly with NWjs.
If it passes Valve's testing process, there should be nothing to worry about anyway. Maybe creating a discussion topic, stating the issue to your customers could help a bit.
With the overlay, if you don't add in --in-process-gpu on the latest version then it doesn't work at all, as in no Steam overlay shows. If you add in --in-process-gpu then all we got was a white screen when trying to view the overlay. It's all working fine on 0.33.3
I have no experience with Greenworks at all, since I'm using Steam4C2. I guess Headbang Games is right and your version simply isn't supported yet.
(PS we are not using any achievements or Steam features on our first release)
Unless you are under pressure because of a publisher or something else, I'd personally really recommend doing things step by step and not rushing it out.