That's a fine question, my guess would be "if" the seal in question has a hole in it, I think the second diagram would apply, (eg: shaft thru hole in seal) but my own question is why do you have two different diagrams for this bike?
Also, did you make note of how it was assembled during the tear down? My 500 K manual is like your first diagram, soo.. I think maybe we need Dave500 or TwoTired to give a definitive answer as to what is going on here.