I think pacstrap, using pacman on the ISO, would need to reference pacman.conf on the ISO.
Looking at pacstrap module in calamares
# postInstallFiles is an array of file names which will be copied into the system
#
# The paths should be relative to the host and the files will be copied to the
# location in the installed system
#
postInstallFiles:
- "/etc/pacman.conf"
- "/etc/calamares/scripts/chrooted_cleaner_script.sh"
- "/etc/calamares/scripts/remove-ucode"
- "/etc/dracut.conf.d/eos-defaults.conf"
- "/etc/nsswitch.conf"
- "/etc/makepkg.conf"