Portage can currently process multiple files in /etc/portage/package.* . This is useful, for example, to have a file containing a bunch of local administrator defaults and then additional file(s) with overrides for that specific host. I think it would be useful if Portage had an option to treat /etc/make.conf similarly. Currently, /etc/portage/make.conf can include files using a "source" line, but that still requires the parent /etc/portage/make.conf be modified to point to it. Allowing /etc/portage/make.conf to be a directory (or automatically processing files in /etc/portage/make.conf.d/ or something) might be useful.
*** This bug has been marked as a duplicate of bug 463266 ***