I needed to add a custom 'install phase:

--8<---------------cut here---------------start------------->8---
       (modify-phases %standard-phases
         (delete 'configure)
         (add-after 'set-paths 'set-sdl-paths
           ;; The makefile adds the output of `sdl2-config --cflags` to the
           ;; compiler flags, but sdl2-config gives us the wrong directory to
           ;; include. We have to add the SDL2 header directory ourselves.
           (lambda* (#:key inputs #:allow-other-keys)
             (setenv "CPLUS_INCLUDE_PATH"
                     (string-append (assoc-ref inputs "sdl-union")
                                    "/include/SDL2"
                                    ":"
                                    (getenv "CPLUS_INCLUDE_PATH")))
             #t))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out")))
               ;; TODO: Install custom .desktop file?  Need icon.
               (install-file "eduke32" (string-append out "/bin"))
               (install-file "mapster32" (string-append out "/bin"))
               (install-file "package/common/buildlic.txt" (string-append out "/share/licenses"))))))
--8<---------------cut here---------------end--------------->8---

I can merge this in your name, let me know.

Playing Duke now!

"Hail to the king, baby!"

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