Well, in Atom you can replace any of the javascript Atom comes with with your own customizations, same in Emacs with elisp, where does the difference lie? (I'm a emacs/evil user).
Emacs is written almost exclusively in elisp, and every elisp function can be changed at any time. Much of Emacs' core lies wide open in the global namespace, and is thus easy to change from any level.
As far as I understand, Atom has quite a bit of code that is not openly accessible, be it because it is part of a Node.js, transpiled from something else, buried in closures, or simply too deep in the hierarchy to be easily reachable from the plugin level. Sure, you could change it if you set your mind to it and maybe patched a few files here and there, but it's certainly not as easy as in Emacs.
