Thanks for your advice. I am not sure if it's good to make the Game.prefs read only, as it may save information on AI-enemies inside (from my understanding).
Using this tip I was able to get vanilla Supcom running at least by altering the start options in steam preferences for the game: %s /windowed 1920 1200
However, FAF does not work yet and still produces the same error, but apparently this issue has to do with starting the game in fullscreen. Maybe this helps in further troubleshooting.