Nice sleuthing, but if that were the case wouldn't the same problem be seen more broadly?
Many don't line up with GeoNames data, but they do appear to be cases where a town name clashes with the name of a local council area, and Apple Maps have chosen the council area instead. Wanneroo is another example here: http://theamazingios6maps.tumblr.com/post/32038150409/wanner...