https://bugs.gentoo.org/232823
http://sources.gentoo.org/cgi-bin/viewvc.cgi/baselayout/trunk/Makefile?r1=3171&r2=3172

--- Makefile
+++ Makefile
@@ -49,8 +49,9 @@
 layout:
 	# Create base filesytem layout
 	for x in $(KEEP_DIRS) ; do \
+		test -e $(DESTDIR)$$x/.keep && continue ; \
 		$(INSTALL_DIR) $(DESTDIR)$$x || exit $$? ; \
-		touch $(DESTDIR)$$x/.keep || exit $$? ; \
+		touch $(DESTDIR)$$x/.keep || echo "ignoring touch failure; mounted fs?" ; \
 	done
 	# Special dirs
 	install -m 0700 -d $(DESTDIR)/root || exit $$?