I don't think zc.catalog and friends were ever officially approved for core; they kind of snuck in as part of plone.app.contenttypes. :-[
A while back I started a RelationIndex package to index relations in the ZCatalog, no matter if they originate as Archetypes references or z3c.relationfield RelationValues or something else. It's only about half done and I lost time/motivation, but I think the approach can work: https://github.com/davisagli/Products.RelationIndex
One advantage to using a separate catalog (true for both AT reference_catalog and the zc.relation catalog) is you can potentially store relations to objects that are not content items. For example, a relation between a portlet assignment and a content item it references. I don't know how many people are doing this in practice.