See summary...
There's some good instructions for this here, btw: http://www.unrealtower.org/fom-serve/cache/80.html I was thinking about wrapping it up into an ebuild one of these days...
The problem is that the Bonus Pack requires one to modify files which are installed by another ebuild. This is a no-no in Gentoo policy. What I am planning on doing is adding a pkg_config section to the ebuild and telling the user that they must run the configuration section manually. This way I do not violate policy and the ebuild is still fairly autonomous. It also keeps from breaking the non-interactive nature of portage. I would have this done already, but work has kept me a bit busy recently.
Man I am a busy boy... I can't believe this has taken me this long to get this added to portage. Anyway, I added it to CVS just now. It appears to work perfectly, from what I can tell. Don't forget to run ebuild /var/db/pkg/games-fps/ut2003-bonuspack-epic-1/ut2003-bonuspack-epic-1.ebuild config as root after your installation. Also, if you've already been playing the game as a user, you will have to run /opt/ut2003/epic-installer as that user before playing the game.