> Back to your snippet — if you still think it's worth trying (to see if
> it gets rid of the ENOENTs), I'll try it and report later.

Starting from guix 3bb3fddb5c6e79056172e5858cdc0ee0b6b8cfaa, I tried
adding this

--8<---------------cut here---------------start------------->8---
#:phases
#~(modify-phases %standard-phases
    (add-after 'install 'customize-texmfcnf.lua
      (lambda _
        (substitute* (string-append #$output "/share/texmf-dist/web2c/texmfcnf.lua")
          (("selfautodir:") #$output)
          (("selfautoparent:") (string-append #$output "/share/"))))))))
--8<---------------cut here---------------end--------------->8---

to `texlive-luatex` as suggested. I verified manually that the file in
the resulting package actually got the paths substituted. I then ran

--8<---------------cut here---------------start------------->8---
guix shell -D guix -- path/to/pre-inst-env guix shell texlive-collection-latex less coreutils grep findutils which strace -C
strace lualatex minimal.tex > strace.txt 2>&1
grep -E 'lualatexquotejobname.*ENOENT' strace.txt | wc -l
--8<---------------cut here---------------end--------------->8---

and got 9138