As Jean pointed most likely the problem with fonts happens because Emacs
from Guix doesn't use fonts from your Fedora font dirs. Installing
required fonts in your user profile will probably fix this issue. You
can do it like this:
guix package -i font-liberation font-dejavu ...
The problem with less bright colors is very surprising for me.
Apparently it is the same "custom theme" in both emacs-es, but it
visibly differs. My only guess is: the theme you use defines different
colors depending on a "class of terminal"/"number of available colors".
But it's probably a bad guess, since it is the same gui emacs in both
cases.
What theme is it? Some derivation of "zenburn" maybe. Could you point
to its source code please?
Do you get 752 after evaluating this: "M-: (length (defined-colors))" ?
You can press "C-u C-x =" on any fontified character and look what face
it is and compare how it is customized/themed for both emacs-es (also
with "C-u C-x =" you can see what font is used by Fedora's Emacs)