Nick, essentially you are asking us to ignore the "The exclude-unlisted-classes element is not intended for use in Java SE environments" part of the spec. This is covered in 8.2.1.6.1 Annotated Classes in the Root of the Persistence Unit of the JPA 2.1 spec, but even JPA 1.0 spec has similar wording.

Which is fine, but this is not a bug. You are just asking for a change in behavior.