They all have to be saved somewhere. A lot of Mac only apps also use the defaults[0] system which allows you to read/write values there.

  man defaults
  defaults domains | tr " " "\n"
  defaults read com.apple.Safari

For dot files, I personally use stow[1] but there are other utilities and workflows out there[2].

  [0] https://ss64.com/osx/defaults.html
  [1] https://www.gnu.org/software/stow/
  [2] https://dotfiles.github.io/