The layers thing is easily explained. Any PDF that has more than one discernible color will have layers, it's part of the process of making a PDF.
Depending on the scanner used and the settings, colors that may look the same will not be scanned as the exact same color, so when the PDF is made, they will be seen as different colors and be put in separate layers. This is easily verifiable if you have a scanner, a PDF maker, and Illustrator.