I've verified that this does indeed affect 5.x still.
However, I cannot edit the 'Affects version' field on this jira, perhaps since I'm not the reporter.

My PR (which contains the SCCE unit tests) against master is up to date, now: https://github.com/hibernate/hibernate-orm/pull/752
failure stacktrace: https://gist.github.com/mattdrees/512d62e3030d7ba6cfeb

If it's helpful, the same tests rebased on the 5.0 branch exist here: https://github.com/mattdrees/hibernate-orm/tree/three-level-derived-identity-5.0 (no PR)

Can someone set the 'Affects version' field to 5.0.2?