Has any paper document you've scanned created a clipping mask?
I just took a scanned paper doc. As tiff or jpeg, opened in Illustrator, I get only Layer1 and ImageLayer. As PDF, I get Layer1, GroupLayer, ImageLayer, ClippingLayer.
As you know there's a lot of variables here - scanner, settings, software/versions - but I believe it is a fact that PDFs opened in Illustrator can have many layers not created by a human. Further, that these layers and layer names match what is seen opening the BC PDF in Illustrator.
So all I'm saying here is that the existence of these layers, as described in the article, does not indicate anything out of the ordinary. They do not indicate any human manipulation; further they more strongly indicate software creation.
Fox has been showing clips of Obama's Oprah segment he taped today. I can't remember his exact words, the gist though is that this was created especially for Obama. Whatever department released this does not normally release them in this"digital" fashion. Which could explain a lot of these otherwise strange placed images.