/etc/portage/env and /etc/portage/package.env are used for modifying Portage's environmental variables, such as those specified in the /etc/portage/make.conf file, on a per-package basis.

The /etc/portage/env directory contains files that have the same syntax as make.conf. The filename will be used as the key to override settings.
The /etc/portage/package.env file describes which of these files will be used on a per-package basis.