Hi Todor,

Indeed, this workaround does the trick.
Here is my ~/.config/fontconfig/fonts.conf:

--8<---------------cut here---------------start------------->8---
<?xml version="1.0"?>
<!DOCTYPE fontconfig SYSTEM "fonts.dtd">
<!-- /etc/fonts/fonts.conf file to configure system font access -->
<fontconfig>
<dir>~/.guix-extra-profiles/emacs/emacs/share/fonts</dir>
</fontconfig>
--8<---------------cut here---------------end--------------->8---

Packages' content is static, it is not modifier upon install, which is
why the default  etc/fonts/fonts.conf is pointing to constant locations.

The solution to this bug, I believe, would be to add a post-install
hook that generates the fonts.conf file with the right entries.

Cheers!

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