Good question! I know some smaller DVD labels have watermarked their transfers of PD titles because even smaller fly by night labels just rip them off. Collections of PD cartoons being an example. Purists hate the bug in the corner of the screen.

It would not surprise me if Criterion found a way to watermark their restoration in a way invisible to the eye and ear.

The recent Manos: The Hands of Fate restoration is copyrighted, but the Blu Ray provides an additional unrestored transfer from a different print with a fair use disclaimer.