The 5 hole papers were in fact punched not in Geneva, but by Rolex USA. I do not think it was an intentional choice to be different, but you will notice that the 5 hole punched papers (the ones that are fully filled out) were always sold in the USA. They started with the "fat green border" papers around the 3 million s/n range, and are most prevalent with the later thinner green border papers, which are actually written in English, with the warranting party listed as "ROLEX USA", not "ROLEX GENEVE". I've noticed however, the watches that come with "double punched papers" are always 6 holes, even when sold in the USA.
Here are some pictures from my archive of sold watches that support this theory. Please keep in mind that a vast majority of the watches I sell are sourced from the public, in which case fake papers would be highly unlikey.