I guess he ran Emacs before checking out his .emacs.d, and Emacs created .config/emacs. Then when he checked out his .emacs.d, it is not loaded. This could confuse some people, for example, when someone installed emacs and ran it once to make sure the install is successful. Adding a notice when creating .config/emacs would be helpful.
This is exactly hat happened. I'm not concerned myself, I understand precisely what's going on. I'm concerned with new users who don't know this stuff yet.
Regards,
Elias