For me it seems that there is a inconsistent declaration where the 'make.conf' should reside: on many documentation links in the installation handbook the referred path is '/etc/portage/make.conf' (e.g. on this page: http://www.gentoo.org/doc/en/handbook/handbook-amd64.xml?part=1&chap=4) and for instance in the x-org how-to as well (http://www.gentoo.org/doc/en/xfce-config.xml).
However, it seems that '/etc/portage/make.conf' takes the priority (read last), but i could not find a statement about 'etc/make.conf' and '/etc/portage/make.conf' in the whole documentation.
And on a fresh and clean installation there's no '/etc/portage/make.conf' for me.
As long as there's no migration, maybe the default system should symlink /etc/make.conf from /etc/portage/make.conf.
If the make.conf on a new installation isn't in /etc/portage then that's a bug in the stage file you're using. As far as I know, the stage3 files provide it in the /etc/portage location already.
$ bzgrep make.conf stage3-amd64-20121013.tar.bz2.CONTENTS
-rw-r--r-- root/root 539 2012-10-13 16:55 ./etc/portage/make.conf
-rw-r--r-- root/root 539 2012-10-13 15:35 ./etc/portage/make.conf.catalyst
-rw-r--r-- root/root 12652 2012-10-13 16:50 ./usr/share/man/man5/make.conf.5.bz2
-rw-r--r-- root/root 19369 2012-10-13 16:50 ./usr/share/portage/config/make.conf.example
If you notice any reference to /etc/make.conf anywhere, I'd be glad to fix it. But I don't see a need to document the old location.