At the end of the day the crew made and error. We all make errors from time to time. Whilst it's important to get to the bottom of it and ensure that everyone (J*, QF, whoever operates airliners with autoflight systems really) learns the lessons gleaned, to my thinking the real issue is the organisational response.
J* protecting the crew by not reporting to the ATSB? If the crew reported the incident then they don't need further protection. It's not like CASA or the ATSB is going to recommend demotion or other sanction along those lines, that's not what the they do in instances like this.
So the question is why wasn't it reported to CASA? Was it a mere oversight and a simple error? If so, what caused the oversight? An overloaded safety department? Time pressures? What about if it was a deliberate decision to not report? Was this due to negligence or deliberate omission? Like a 'choose your own adventure' book the answers to each of these questions leads to various outcomes. Most of those outcomes are very unpleasant and none of them paint a pretty picture of the organisational culture.
What is most interesting is how quickly things can go from being 'stable' to seriously out of shape. A reminder for all of us that no matter whether you're a LCC or a 'legacy' carrier that aviation is very unforgiving and that no one has a mortgage on being error free.