Maybe we could do like this in base-files.bb ?

FSTAB_HAVE_WIC = "${@bb.utils.contains('IMAGE_FSTYPES', 'wic', 'true', 'false', d)}"
FSTAB_WIC_UPDATER = "${@bb.utils.contains('WIC_CREATE_EXTRA_ARGS', '--no-fstab-update', 'false', 'true', d)}"

do_install:append() {
if [ ${FSTAB_HAVE_WIC} = true ] && [ ${FSTAB_WIC_UPDATER} = true ]; then
sed -i '/\/dev\/root/d' ${D}${sysconfdir}/fstab
fi
}

This would remove the hardcoded '/dev/root' entry  if all conditions are met to add the root entry with wic fstab-update
It˙s looking like the easiest fix here is to revert your patch, so at least we don˙t have warnings and unexpected behaviour on boot. Unless you˙re willing to rework your patch so that it allows edits to the root mount point but doesn˙t end up creating duplicates?