I'd like to suggest adding a section to the later stages of the final configuration to include having the user do an emerge -u system with an explanation of how to handle config file changes. I'll write it if you want. :)
which config files are you refering to ? the FAQ and Desktop guide are pretty good places for users to start ... http://www.gentoo.org/doc/faq.html http://www.gentoo.org/doc/desktop.html
I made a note of this in the build howto. I informed the reader that they should run etc-update before unmounting the partitions and rebooting. //ZhEN