Hibernate entitymanager only evaluates an orm.xml file in the META-INF directory of root of the persistence unit but no orm.xml file from the META-INF directory of any jar file referenced by the persistence.xml.
The ejb3 spec says that all orm.xml should be evaluated (-> "JSR 220: Enterprise JavaBeansTM,Version 3.0 Java Persistence API", chapter 6.2.1.6).
Hibernate forum topic: http://forum.hibernate.org/viewtopic.php?p=2334504#2334504