There are plenty of ways of explaining the results of qualifying at Phillip Island. Lack of set up time in consistent conditions make the qualifying order a bit of a lottery. Rain and wind coming in off the Bass Strait and the weather changing every minute or so meant getting your timing and strategy right was crucial. Changing track conditions and unpredictable weather meant that some teams gambled right on whether to have their bikes in a wet set up, on intermediates, or on slicks. Or even on the correct mixture of tires front and rear.
In reality, though, the main factor in determining the qualifying order was this: the temperature in the front tire. Riders who could generate it had confidence in the front and could push hard in the sketchy and cold conditions. Riders who couldn't, languished well down the order, unable to feel the front and unable to lap with any confidence or feedback from the tires.
That explains why Marc Márquez and Cal Crutchlow are on the front row of the grid at Phillip Island, while the factory Yamahas languish back in twelfth and fifteenth place (or "on the fourth and fifth row of the grid" as it is known in press release speak). The Hondas have a tendency to overheat the tires due to the way they brake and their geometry. The Yamahas lean heavily on the front tire to generate corner speed, and on the edge of the rear tire to maintain it. At Phillip Island, it was too cold and too windy to do either.