That's not exactly what emacs does: if ~/.config/emacs isn't there, then it will default to creating ~/.emacs.d/ and ~/.emacs, even if the XDG env vars are set. Basically, emacs supports XDG config if you really want it to, but it's not the default way of using emacs. And of course, it only uses ~/.config/emacs, none of the other XDG folders. If you download a package from MELPA, that's still going to .config/emacs, as far as I know.