It's unfortunate that the thread seems to have got itself confused between a punctuality analysis and a safety study.
As far as the former is concerned, the methodology and data seem pretty sound, but I agree that the results need to be interpreted with caution.
As regards the safety study, it's put together by the Australian provincial newspaper that runs the airlineratings com website (generally regarded as a bit of a joke in the industry) so we probably shouldn't be too surprised that Qantas gets first place.