The majority of configuration files should not be edited directly, but changed by changing settings in the app preferences. So that seems consistent with the philosophy on the Mac - don't work with files and the file system directly, but let the appropriate app take care of it as far as possible. Same with music and photos.

Photos existing in the giant photos thing is just a mess. I hate it. I have to export them to do anything. I am not sure they even back up correctly. And this is photos.