I think it would be a good idea to add rm "${S}"/xml/expat/buildconf.sh before ./buildconf line to all of the current ebuilds. That change doesn't break anything, as we are are using system expat and running that script is guarded by test of its existence, it generates only noise and doesn't work properly with libtool 2 anyway. For confirmation, simply read buildconf.
i think it would be a good idea to not run buildconf at all since it doesn't break anything. fixed in cvs, thanks