>=portage-2.2_pre6 installs make.globals in /usr/share/portage/config. /etc/make.globals is a symlink to /usr/share/portage/config/make.globals, but somewhen in future portage ebuilds might stop installing /etc/make.globals, so eix should first try to read /usr/share/portage/config/make.globals and if it doesn't exist, then eix should read /etc/make.globals.
Thanks. In current eix svn trunk (>=eix-0.12.5) MAKE_GLOBALS is introduced which defaults to %{EPREFIX}/usr/share/portage/config/make.globals. If this is a file, it is read instead of %{PORTAGE_CONFIGROOT}/etc/make.globals
Closing since eix-0.12.5 is in the tree now.