Certainly! If you add my latest Kirk/Spock slash fanfic to the end of the text, then that is transformative, so the resulting PDF is covered under copyright.

But you wrote "scan". Adding an OCR'ed text layer, or doing manual proofreading and layout ("sweat of the brow") is not sufficiently transformative to have copyright protection.

And we were specifically talking about scans of old books stored in shadow libraries.