If you're clearing all the game files (aka uninstalling the game), the uninstall process should be able to clear the registry without the user having to touch it. If you're trying to edit game settings without opening the game, that's literally what a config FILE is for.
I'm perfectly comfortable editing the registry myself, although I'd much rather not mess with it even so; I've worked in IT and know what not to touch. The problem is that most people don't know what not to touch. Changing game settings in the registry won't brick your computer, correct. However, if you don't know what you're doing, it's unfortunately quite easy to click the wrong thing and break something unrelated to the game. I stand by my statement that 90% of computer users, including gamers, have no business even knowing the registry exists, much less editing things in it.
What really blows my mind is that there was a config file, but the devs decided that directly editing the registry is better idea somehow.