/var/www/localhost/htdocs/twiki_install_directory/pub needs to have FollowSymLinks set so that (at minimum) the themes work. Other things may be broken, but this is the method by which Apache2's error_log suggested I fix it. Important to note that my /usr/share/webapps and /var/www/website/htdocs are on two different filesystems, so webapp-config will create the symlinks during install instead of the hard-links, which the default configuration assumes. Probably a good idea to suggest that it's set anyway. Included is a diff for twiki_httpd_conf.txt in /twiki_install_dir 61c61 < Options None --- > Options FollowSymLinks
I don't think we should push these instructions down to individual ebuilds (we would basically have to add a similar warning to most ebuilds in the tree). The issue with symlinks is already documented in man webapp-config.