If cfg-update is executed (by the root user) and it does not find a /root/.bashrc file then it creates one itself. The file it creates is a copy of gentoo's /etc/skel/.bashrc from 2003(!) and is rather outdated. Furthermore, this file is not sourced anyway because by default there is no /root/.bash_profile which is the one that actually sources the .bashrc file. I think there is no reason for cfg-update to create that file.
Ok, I've been bugged by this as well. This is a leftover from the pre-hook days. I removed it entirely in 1.8.8, which you can install from my overlay. If it works fine in my testing for a few days I'll put it in portage.
