All installers install the executable to internal memory (or whatever filesystem your booting off of).

The mmc1 and mmc2 installers only change the start script to look for data files on the respective mmc locations.

You cant copy an executable to a FAT formatted filesystem and execute it since that filesystem is mounted noexec. The only alternative i offer is my iso appliance which packs all files into an iso which you can store on a FAT filesystem, and execute like a rom but this is harder to copy pak files into and configure autoexec since you have to repack the ISO.

You can also create an ext2 filesystem which you can run programs off of, store that ext2 fs as file on fat mmc and mount it but when you reboot you'll need to remount.

Oh yea, and if your booting of mmc and want the data files to go there then install the ready2run version and put paks into /usr/lib/sdlquake