Althought dbus-1.0.2-r2 with USE="doc" puts app-doc/doxygen and app-text/xmlto into dependencies, it never uses them. For doxygen I couldn't find make target to build documentation (no, --enable-doxygen-docs does not make it being build just checks for doxygen), so I can explicitly. As for xml, --enable-xml-docs turns *.xml files in doc/ into *.html, so I guess we want it, as it provides such interesting file as dbus-tutorial.html, etc.
Created attachment 132070 [details, diff] Proposed patch.
Should be fixed in 1.3.0-r1. Feel free to reopen if it's still causing you problems.