This issue isn't completely solved with version 5.x (we have specifically version 5.2.10.Final). If the SequenceGenerator is defined in orm.xml mapping-file, then the schema is not used and same exception as described is thrown.
I think the problem could be solved with one line in org.hibernate.cfg.annotations.reflection. JPAOverriddenAnnotationReader in method buildSequenceGeneratorAnnotation(Element element), where schema is not read.