Ebuilds repeatedly try to assign to EXTRA_ECONF and EXTRA_EMAKE. In order to prevent that, please make these variables read-only as soon as their values are supposed to be set (i.e. after sourcing bashrcs and /etc/portage/env files).
I'm planning to do this as a repoman check, in case people want to modify these variables in things like bashrc / phase hooks.
This is fixed in git: http://git.overlays.gentoo.org/gitweb/?p=proj/portage.git;a=commit;h=a0adfb21ec64da8013265adfb2ed9ffb18e6a2b4
This is fixed in 2.1.11.25 and 2.2.0_alpha136.