I managed to generate a bootable iso.
The magic is that the build-iso.sh script needs to run in a guix system as opposed to a Debian system with the guix package manager installed.
I was able to use the guix package manager in Debian to install the nonguix system on an external ssd. After booting the nonguix system on the external ssd the build-iso.sh script finishes with success.
Next problem is that the installation from that iso still installs the limited gnu kernel.
So far it seems that a successful approach is to enable nonguix on the debian system and install from there into another partition. Without the help of an installer you need to generate a config.scm yourself.