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...
The gist for me is that you need local offices for mapping quality control. Probably the best option for apple would be to set up a mapping office inside each of their Apple stores.