If I read JAXB 2.2 5.5.2.2 correctly it's correct that the CollectionPropertyHandler first calls List<Type> getId() to see if a collection exists. (In fact it says a setter is not allowed.)
To solve the problem at hand, PersistenceMetaData should return a 'managed' list which keeps track of additions. Similar to EnterpriseBeansMetaData. With some helpers it could probably be the list itself.