I discovered a nice property of AC_CONFIG_AUX_DIR and (CVS) Automake: you can use the Autoconf macro, and not provide a Makefile.am for this directory. The content is properly shipped, everything works fine, and you saved one AC_CONFIG_FILES, one Makefile.am, one SUBDIRS.
I don't know if this is will be preserved, but I would suggest that the decision to support or not to support this feature be specified. If positive, then let's document, if not, let's add a warning somewhere.