`ebuild` ignores FEATURES="userpriv" and FEATURES="-userpriv" set in environment (and respects value from /etc/make.conf). `emerge` doesn't ignore values from environment.
This seems to fix it: http://git.overlays.gentoo.org/gitweb/?p=proj/portage.git;a=commit;h=9f9763896a887d375a59b167f96019a3c0a0b9bc
This is fixed in 2.1.9.47 and 2.2.0_alpha31.