Hi perhaps I am being a bit naive when I suggest this but that setup thing is just a script / set of scripts as far as I know.

The source is https://github.com/RetroPie/RetroPie-Setup . You could just see what they do and create a script to run whatever you wanted instead. You could for example get the git repository and create your own script to run (instead of retropie_setup.sh) to do what you need.

I’ve only looked briefly at the scripts to see what version of moonlight it was using. Anyway, to me seems quite trivial to do.