I'm also studying the topic, and reaching some conclusions, but I am not an expert so I appreciate any correction
Hibernate is a JPA 2.0-compliant superset from version 3.5 on if I recall correctly. Latest 4.x versions are candidates for JPA compliance 2.1 from what I read.
Anyway, htere is a flag to configure it for ouputing JPA annotations alone (in the case of Hibernate Tools for Eclipse, you are asked in Launch configurations menu) and even add some EJB3 to the mix, for pure standard compliance
If you do the reverse-eng generation with the "Core" flag, it seems to map to cfg XMLs, if you use "Annotations", it outputs Hibernate's org.hibernate.* annotations, but with "JPA" you are entirely using javax.persistance.* ones, at least for those basic things as I checked so far.