Another factor which often irks me is that schools will set up their high school curriculum in a manner that inflates these statistics artificially. One key example I can think of which supports this is my former school mandating that anyone who does 1/2 Spec (or GMA, whatever it's called) do 3/4 Further Maths simultaneously in their own, secluded cohort. What this means is that the overwhelming majority of the class can pick up a score in at least the low 40s, bumping up the number of 40+ scores in terms of the overall percentage. Sure, the ulterior motive that I'm suggesting exists might not be the only reason, but considering that these are students who won't even get to have three maths subjects in their top 4, it wouldn't appear to be of great benefit to the students themselves. I hope you can see what I'm suggesting here.
Similarly, scores have been bumped up by having Year 11 students only be allowed to accelerate subjects which are traditionally 'easier' to score an unscaled 40+ in, such that the overall percentage is, again, inflated. Consider that any Year 11 who completes a 3/4 subject a year earlier generally dedicates extra time and effort into these subjects, and combine this with the fact that they will be completing subjects such as HDD, P.E, Psychology, and Further Maths, and you end up painting a picture to the outside world that the VCE scores of a cohort are higher than what they actually are. Not to mention: students can't complete subjects such as Methods, LOTE German/Jap, or Chemistry a year early.
At the end of the day, these 'artificial boosts' could be considered negligible in the grand scheme of things, and they won't really be effective unless the school is already academically capable enough. However, they do illustrate how the statistics used to rank schools can be extraordinarily misleading, and hinge so much on the flaws of a VCE system which can be adapted to a school's preferences in order to make them appear better than is truly the case.