diff --git a/Makefile b/Makefile
index b8678ea15b..77ca3b4702 100644
--- a/Makefile
+++ b/Makefile
@@ -782,17 +782,10 @@ endif
 # For a merged /usr, ensure that /lib, /bin and /sbin and their /usr
 # counterparts are appropriately setup as symlinks ones to the others.
 ifeq ($(BR2_ROOTFS_MERGED_USR),y)
-
-	$(foreach d, $(call qstrip,$(BR2_ROOTFS_OVERLAY)), \
-		@$(call MESSAGE,"Sanity check in overlay $(d)")$(sep) \
-		$(Q)not_merged_dirs="$$(support/scripts/check-merged-usr.sh $(d))"; \
-		test -n "$$not_merged_dirs" && { \
-			echo "ERROR: The overlay in $(d) is not" \
-				"using a merged /usr for the following directories:" \
-				$$not_merged_dirs; \
-			exit 1; \
-		} || true$(sep))
-
+	@$(call MESSAGE,"Sanity check in overlays $(call qstrip,$(BR2_ROOTFS_OVERLAY))")
+	support/scripts/check-merged-usr.sh \
+		--type overlay \
+		$(call qstrip,$(BR2_ROOTFS_OVERLAY))
 endif # merged /usr
 
 	$(foreach d, $(call qstrip,$(BR2_ROOTFS_OVERLAY)), \
diff --git a/package/skeleton-custom/skeleton-custom.mk b/package/skeleton-custom/skeleton-custom.mk
index b05c834b94..c194108307 100644
--- a/package/skeleton-custom/skeleton-custom.mk
+++ b/package/skeleton-custom/skeleton-custom.mk
@@ -26,17 +26,16 @@ endif
 # For a merged /usr, ensure that /lib, /bin and /sbin and their /usr
 # counterparts are appropriately setup as symlinks ones to the others.
 ifeq ($(BR2_ROOTFS_MERGED_USR),y)
-SKELETON_CUSTOM_NOT_MERGED_USR_DIRS = \
-	$(shell support/scripts/check-merged-usr.sh $(SKELETON_CUSTOM_PATH))
+define SKELETON_CUSTOM_NOT_MERGED_USR_DIRS
+	support/scripts/check-merged-usr.sh \
+		--type skeleton \
+		$(SKELETON_CUSTOM_PATH)
+endef
 endif # merged /usr
 
-ifeq ($(BR2_PACKAGE_SKELETON_CUSTOM)$(BR_BUILDING),yy)
-ifneq ($(SKELETON_CUSTOM_NOT_MERGED_USR_DIRS),)
-$(error The custom skeleton in $(SKELETON_CUSTOM_PATH) is not \
-	using a merged /usr for the following directories: \
-	$(SKELETON_CUSTOM_NOT_MERGED_USR_DIRS))
-endif
-endif
+define SKELETON_CUSTOM_CONFIGURE_CMDS
+	$(SKELETON_CUSTOM_NOT_MERGED_USR_DIRS)
+endef
 
 # The target-dir-warning file and the lib{32,64} symlinks are the only
 # things we customise in the custom skeleton.
@@ -49,9 +48,7 @@ define SKELETON_CUSTOM_INSTALL_TARGET_CMDS
 endef
 
 # For the staging dir, we don't really care what we install, but we
-# need the /lib and /usr/lib appropriately setup. Since we ensure,
-# above, that they are correct in the skeleton, we can simply copy the
-# skeleton to staging.
+# need the /lib and /usr/lib appropriately setup.
 define SKELETON_CUSTOM_INSTALL_STAGING_CMDS
 	$(call SYSTEM_RSYNC,$(SKELETON_CUSTOM_PATH),$(STAGING_DIR))
 	$(call SYSTEM_USR_SYMLINKS_OR_DIRS,$(STAGING_DIR))
diff --git a/support/scripts/check-merged-usr.sh b/support/scripts/check-merged-usr.sh
index 6d31c81c21..c3b5c6419a 100755
--- a/support/scripts/check-merged-usr.sh
+++ b/support/scripts/check-merged-usr.sh
@@ -11,16 +11,48 @@
 # /usr/sbin/
 #
 # Input:
-#   $1:     the root directory (skeleton, overlay) to check
+#   --type TYPE     the type of root to check: 'skeleton' or 'overlay'
+#   $*:             the root directories (skeleton, overlays) to check
 # Output:
-#   stdout: the list of non-compliant paths (empty if compliant).
+#   stdout:         the list of non-compliant paths (empty if compliant).
 # Exit code:
-#   0:      in case of success (stdout will be empty)
-#   !0:     if any path is improperly merged
+#   0:              in case of success (stdout will be empty)
+#   !0:             if any path is improperly merged
 #
 
-# The directory to check for merged-usr
-root="${1}"
+opts="type:"
+ARGS="$(getopt -n check-merged -o "" -l "${opts}" -- "${@}")" || exit 1
+eval set -- "${ARGS}"
+
+type=
+while :; do
+	case "${1}" in
+	(--type)
+		type="${2}"
+		shift 2
+		;;
+	(--)
+		shift
+		break
+		;;
+	esac
+done
+
+report_error() {
+	local type="${1}"
+	local root="${2}"
+	local fmt="${3}"
+	shift 3
+
+	if ${first}; then
+		printf "The %s in %s is not properly setup:\n" \
+			"${type}" "${root}"
+	fi
+	first=false
+	# shellcheck disable=SC2059  # fmt *is* a format string
+	printf "  - ${fmt}" "${@}"
+	is_success=false
+}
 
 # Extract the inode numbers for all of those directories. In case any is
 # a symlink, we want to get the inode of the pointed-to directory, so we
@@ -42,19 +74,24 @@ is_valid_merged() {
 }
 
 test_merged() {
-	local root="${1}"
-	local dir1="${2}"
-	local dir2="${3}"
+	local type="${1}"
+	local root="${2}"
+	local dir1="${3}"
+	local dir2="${4}"
 
 	if ! is_valid_merged "${root}" "${dir1}" "${dir2}"; then
-		printf '%s\n' "${dir1}"
-		is_success=false
+		report_error "${type}" "${root}" \
+			'%s should be missing, or be a relative symlink to %s\n' \
+			"${dir1}" "${dir2}"
 	fi
 }
 
 is_success=true
-test_merged "${root}" "/lib" "/usr/lib"
-test_merged "${root}" "/bin" "/usr/bin"
-test_merged "${root}" "/sbin" "/usr/sbin"
+for root; do
+	first=true
+	test_merged "${type}" "${root}" "/lib" "/usr/lib"
+	test_merged "${type}" "${root}" "/bin" "/usr/bin"
+	test_merged "${type}" "${root}" "/sbin" "/usr/sbin"
+done
 
 ${is_success}