dev-util/gtk-doc-am directly depends on dev-util/pkgconfig instead of using virtual/pkgconfig. Was this done intentionally, because it wouldn't work with the other alternatives which provide virtual/pkgconfig, or is it just a mistake?
virtual/pkgconfig was created 4 days ago. There were thousands of ebuilds in portage that depended on dev-util/pkgconfig, and you cannot expect all of them to be updated instantly. In any case, gtk-doc-am was already fixed in cvs a few hours ago.
Oh, sorry, I didn't realize virtual/pkgconfig was that young... And about those "thousands of ebuilds": It was the only ebuild on my two systems - I wouldn't have reported this otherwise.