Not sure about true fullscreen, I've tried changing launch options in steam, but they seem to be unrecognised, I think the easiest way is to change to an Aero theme, just save your current theme and change to Aero when you want to play Factorio.
I had issues playing Fallout 4 aswell.

I had the same problem, I changed the desktop wallpaper to an Aero theme, and it fixed it, I am however still using Win 7, I'm not sure if you are on Win 10 or not.