If I try to run emerge --info atom, where atom is a package listed in package.env (and with different variables from normal make.conf), emerge show me normal variables (from make.conf) instead of the one in /etc/portage/env/ . Actually portage install that package as specified in separated env, just doesn't looks like when --info is called Reproducible: Always
*** This bug has been marked as a duplicate of bug 410069 ***