https://www.gnu.org/software/emacs/manual/html_node/emacs/Fi...
I do know that ~/.emacs takes precedence over ~/.emacs.d/init.el. I've taken advantage of that in the past to keep all the public configuration that I share between machines in ~/.emacs.d/init.el, and then on my work machine I had a ~/.emacs that wraps a (load "~/.emacs.d/init") with some company-specific configuration.