docbook2X and docbook-sgml-utils seem to install the same files. I do not know which one is superior, though my hunch is that the latter is. Either way, please make it so that the installed-files-lists are unique for them. (ie, if docbook2X is not even necessary, then just mask it or increase the -r to have it emerge docbook-sgml-utils, etc).
addendum -- if docbook2X is not needed, then use the move functionality -- see /usr/portage/profiles/updates/3Q-2002 for how to achieve that
Now everything is installed as .pl for docbook2X, as that's the less widely used one, not even depended on by anything that really needs it as opposed to docbook-sgml-utils...