Originally Posted by AustinChief
I don't know every scanner out there but any scanner (ie a Xerox WorkCentre) that uses MRC will automatically creates multiple rasters that will show up as layers in Illustrator when the PDF is imported. That alone should really lay this to rest.
Of course, if any .pdf has layers, you can open a .pdf with all it's layers intact in Illustrator. Even if the document is created originally in Illustrator and saved as a .pdf depending on what command you use to open it.