I think, the best way is to fix the documentation. The reason is, when a developer rely to the behavior of the function but the behavior is changed, a program may work incorrect.

Just think about forensic stuff. If a hash value will be created with the "parsebytes" method and the behavior will be changed to match the behavior of the "parse" method, the the evidence can not be validated with the latest python versions.

We could add a comment to the documentation. For example "parsebytes parses the mail in a different way than parse, which may produce slightly different messages. If you rely on the same behavior for file and byte like objects you can use the parse method with BytesIO"