The issue with this has always been during the initial shooting of the photos for each course.
Frankly I would think you would map 3 sets of pins for each course, since that gives you three different versions of each green to play.
I do also agree for whatever reason these pin placements don't pop up on a regular basis, I would suggest that we see some 5 times more than others. For example how often do you see the up pin on hole 11 at St Andrews and how often do you see the back pin on hole 15 at Beth Page.
I'm sure there is a reason but I don't know it.