There is a disconnect between the full Spring Mongo documentation and spring-mongo-1.0.xsd (also spring-mongo-1.1.xsd.) Essentially, the XSD says that when declaring a <mongo:db-factory> element, the default value for the mongo-ref attribute is mongo, implying that if you declare no mongo-ref attribute, the configuration will reference any existing <mongo:mongo /> element for further configuration of mongo. However, that is not the case. As the full documentation states, you must declare this mongo-ref if you want to use another mongo instance (with advanced options for example) instead of the one configured by <mongo:db-factory />.
tl;dr - The XSD description of the db-factory element should be changed from "The reference to a Mongo. Will default to mongo." to something more accurate, such as "The reference to a Mongo. Set this value if you need to create a more advanced Mongo beyond the capabilities of the db-factory element." =)