FWIW, I did report the issue in github for epubcheck 4.0.1 and they have acknowleged a bug and said a fix would be in the next release.
See:
https://github.com/IDPF/epubcheck/issues/680
Betrand, you might want to add your test results above as they are quite conclusive proof of a bug as my hypothesis was just based on eyeballing the code. It would allow them to easily create a testcase to prevent future reversions.
Take care,
KevinH