Checking the source, Portage.pm line 50 reads foreach my $file ( "$ENV{HOME}/.gcpanrc", "/etc/make.conf", "/etc/make.globals" ) { Since /etc/portage/make.conf seems to be encouraged these days, it should also be in the search list.
https://github.com/gentoo-perl/g-cpan/pull/1
Patched in 0.16.4-r1 waiting for a whole new release or something.
+*g-cpan-0.16.5 (14 Jul 2014) + + 14 Jul 2014; Tony Vroon <chainsaw@gentoo.org> +g-cpan-0.16.5.ebuild: + Release incorporating fixes from bugs #420617, #424657 & #484108. With both + my thanks and my apologies to Sergiy Borodych, Roberto Araneda & Petr Pisar.