Yes, you are right. PersistenceException is a RuntimeException and as such is a system exception from the EJB Container's point of view. However, don't forget that it is NOT an EJBException.
If your application uses session or mesage-driven beans and a call to an EntityManager method throws a PersistenceException (and if the bean rethrows that exception), the EJB Container will wrap the exception in an EJBException and rethrow it to the bean's client. Also, the bean will be discarded (as it is a system exception) and the transaction will be rolled back: in all cases(!), even if the PersistenceException was in fact a NonUniqueResultException or NoResultException. The reason behind that is that when the bean rethrows the PersistenceException, that is regarded as a system exception from the EJB Container point of view (and we know what happens with system exceptions).