Not quite the scenario described (it wasn't an academic paper), but https://mjg59.dreamwidth.org/73317.html is my experience of dealing with a forged PDF. Part of the reason it's rare is that it's actually very hard to do it well!
I believe it's actually linked in the OP about half way down. What a crazy thing for an agent to do - to turn a minor disagreement into a maybe-crime.
Are you saying that RightSignature puts the checksum information inside the document and therefore destroys the checksum? What is the thinking behind that?