Using heel raises in the early stages of teaching the back squat is fine. This teaches proper depth and also recruits all of the quadriceps muscles to a greater degree. Once the athlete has adpated to this then the raise can be removed or reduced until optimal squatting is achieved.
Also I am sure improper dynamic flexibility is not the source of evil for NRL injuries. If a movement is performed incorrectly in a warm-up there is no logic behind explaining that they would strength train incorrectly as well. In the warm-up for an NRL match I am sure players would not be concentrating on their lumbar spine positioning, but rather winning the match.