I had a situation with The Saboteur.
When installed manually with downloaded installers it had configuration issues, IIRC it was limited to 1280x720 and the in game option to modify it didn’t work.
But when installed with Galaxy it defaulted to 1920x1080 and the in game options worked.
At that point my game was working and I didn’t investigate further so I don’t know if it was downloading different installers, or performing post install tweaks to my game config, but from a functional perspective the game was broken when not using Galaxy. Ideally whatever the “magic” was it should be included in the standalone installers!