build-docbook-catalog from app-text/build-docbook-catalog should be modified to use update-xmlcatalog from dev-util/xml-core instead. The reason for this is update-xmlcatalog keeps a separate database in /var/lib/xml-core of the catalogs and writes them to /etc/xml completely destroying any changes that xmlcatalog would have made in /etc/xml directly. This incompatibility is documented in the update-xmlcatalog manpage. Reproducible: Always
Since there are already packages and ebuilds in gentoo that depend on xmlcatalog, it's probably better to continue depending on xmlcatalog instead.