Looking good!

I just tried to install Emacs to a dummy profile with your patch.
Here is the result (with ":" replaced by line breaks):

--8<---------------cut here---------------start------------->8---
...
export EMACSLOADPATH=\
"${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/site-lisp/
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp/
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//calc
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//calendar
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//cedet
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//cedet/ede
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//cedet/semantic
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//cedet/semantic/analyze
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//cedet/semantic/bovine
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//cedet/semantic/decorate
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//cedet/semantic/symref
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//cedet/semantic/wisent
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//cedet/srecode
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//emacs-lisp
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//emulation
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//erc
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//eshell
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//gnus
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//image
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//international
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//language
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//leim
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//leim/ja-dic
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//leim/quail
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//mail
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//mh-e
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//net
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//nxml
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//obsolete
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//org
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//play
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//progmodes
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//term
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//textmodes
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//url
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/26.3/lisp//vc
${GUIX_PROFILE:-/gnu/store/g5371rkr7k5j6n5gmg0a8bhspsdfnjvy-profile}/share/emacs/site-lisp/${EMACSLOADPATH:+:}$EMACSLOADPATH"
export ...
--8<---------------cut here---------------end--------------->8---

Then I did

--8<---------------cut here---------------start------------->8---
/home/ambrevar/projects/guix/pre-inst-env guix environment --ad-hoc emacs emacs-expand-region -- emacs -q
--8<---------------cut here---------------end--------------->8---

And I get Emacs with expand region functions, but since GUIX_ENVIRONMENT
is still effective, it's unclear what loads it.

So it seems to be the right approach, let's keep testing!

With regard to the "cleanups" you mentioned:

> Various cleanups could be undertaken in both Guix (no longer need the
> set-emacsloadpath phase in the emacs-build-system) and Emacs-Guix (no
> need for custom logic looking into ~/.guix-profile) and perhaps other
> places should this get merged.

Shall we keep guix-emacs.el (and site-start.el) at all?

What guix-emacs.el does if I'm not mistaken:

- Find autoloads: Would we still need this then?  I'm not sure.  If
  not, then it would be great to remove this because finding-autoload
  linearly increases Emacs loading time.

- Find packages in GUIX_ENVIRONMENT: I suppose we don't need this since
  EMACSLOADPATH should be in the `guix environment' as well.

- Find packages in "/run/current-system/profile": The approach used by
  other programs at the moment is to do this in /etc/profile, e.g.

--8<---------------cut here---------------start------------->8---
export MANPATH=\
$HOME/.guix-profile/share/man\
:/run/current-system/profile/share/man
--8<---------------cut here---------------end--------------->8---

Seems to me that we can remove guix-emacs.el and site-start.el.

Cheers!

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