The bug was investigated by the NW.js team and then reported further to the Chromium team by Ashley and it looks like we have the solution!
Based on suggestion from the Chromium team I made some tests with the --disable-direct-composition Chromium option. I cannot replicate screen flickering any more while using this option. More over this option fixes also the Recording gameplay issue (NWjs, youtubers) issue.
I asked Chromium team about consequences of using this option. It disables the DirectComposition component which in theory should reduce the app performance by around 10%. However I could not notice any performance drop while testing it with my game so the performance drop is indeed not big.
For those who are not familiar of how to set up Chromium args in C2, here's a short tutorial:
1. Go to {your C2 directory}\exporters\html5\nwjs
2. Open package-win.json file with any text editor
3. Add "--disable-direct-composition" to the chromium-args section
4. You may also want to add it to the package-preview.json to have it fixed also in preview mode
I don't know if this is the final solution or Chromium team will fix DirectComposition feature. But For now is a very decent solution which fixes very serious (in my opinion) issues with C2 PC apps.
Once again thank you TheRealDannyyy, —, MadSpy and all for your support in solving this issue