run into it - when I run eix-update yesterday within a chroot image (probably run it as portage:portage ?) -- it doesn't read that file, therefore it ignored the PORTDIR_OVERLAY directory at least I'd expect an error message
It is not an error to have no or unreadable make.conf - especially, since there are different locations for it like /etc/make.conf and /etc/portage/make.conf, and users of other package managers (paludis) usually have neither. Moreover, for portage overlays are often set in /etc/portage/overlays.conf instead of make.conf.
