The problem isn't the db-factory, it's the mapping-converter that has an optional argument "db-factory-ref". This argument is internally preset to "mongoDbFactory" to match the default "id" of the db-factory.
So the "id" of the db-factory works, but the "db-factory-ref" of the mongo-conver has to be set accordingly:
<mongo:db-factory id="xmlDbFactory" ... />
<mongo:mapping-converter db-factory-ref="xmlDbFactory">