With the gamescope util, the %command% would be the path to the game exe/bin that's usually there?
Yes, but you also leave it as-is. Steam replaces it for you, so basically gamescope -w1280 -h720 -W1920 -H1080 %command% in the launch options would AMD FSR upscale the game from 720p to 1080p and Steam will fill in %command% with whatever it needs to run Proton and then the game in it. Just need to make sure the options are between gamescope and %command% for them to be interpreted correctly.