Desktop settings package should only install stuff to /etc/skel for the most part. If you need to overwrite system files, you should use the desktop-overlay/etc/greetd/config.toml in the iso-profile. Note that overlay is only for overwriting files, you should avoid putting there anything that is not provided by some package.
Services are enabled in profile.conf in the iso-profile. Since greetd is not directly supported yet, set the the display manager to none and just put the greetd service to the right array.
If you need to configure autologin for the live session, do so by using the live-overlay directory.
Can you upload the PKGBUILD for the desktop settings somewhere?