I encountered a similar issue while trying to package something with a texlive-union input. Tracking down the issue has killed way too many hours.

FWIW, the `working.tex' minimal example is also giving me similar problems:

    $ guix describe
    Generation 28    5月 07 2020 01:10:02   (current)
      guix bed695a
        repository URL: https://git.savannah.gnu.org/git/guix.git
        branch: master
        commit: bed695aa94cd85800ec2c6296fb2d13e7ac29133
    $ guix environment --pure -e '((@ (gnu packages tex) texlive-union) `(,(@ (gnu packages tex) texlive-amsfonts)))'
    $ pdflatex working
    ...
    ! Math formula deleted: Insufficient symbol fonts.
    \)  ->\relax \ifmmode \ifinner $
                                    \else \@badmath \fi \else \@badmath \fi
    l.4 Hello! \(y = x^2\)
    ...

With the patch to texlive-amsfonts the above typesets just fine; however, metafont ends up generating cmmi10.657pk and cmr10.657pk font files. Is this expected? Typsetting it from the texlive installation of my foreign distro doesn't call out to metafont at all.