Well, it's actually not.

I'm a happy Steam user, but it has quirks. Steam has issues with some games and their mods. Medieval Total War 2: Kingdoms, for instance. Creative Assembly put out a realism mod that I was dying to try. It was linked through the game-launcher itself. Updating the game to include the mod, though, changed the .exe and invalidated the install. And it's not unheard of for other mods to change the .exe.

Steam is getting better with issues like that, but they still exist.