Great work, looks like you are getting close to the finish line! :)

> I'll rework the 'gnu: emacs: Remove custom guix-emacs code.' patch, as
> removing it means losing having the autoloads definitions loaded.
> Someone in the #emacs channel suggested making use of the builtin
> package.el code to take care of this.  To be continued :-)

Indeed, this is the normal workflow using package.el.  See
https://melpa.org/: the user is expected to call `package-initialize`
from their init file.

So the solution is quite simple I believe: add

--8<---------------cut here---------------start------------->8---
(require 'package)
(package-initialize)
--8<---------------cut here---------------end--------------->8---

to site-start.el.

Cheers!

-- 
Pierre Neidhardt
https://ambrevar.xyz/