Pilots like to read a report and find something they would not have done so they can rationalize "That wouldn't happen to me." But it's not a controversial idea that accidents have a chain of causes that together led to the accident i.e the swiss cheese model.
The pilot's actions were analyzed in detail in the report. The Class C controller denying clearance was another link.
But I think there was confusion between the Class D controller and the pilot that was significant, and that wasn't examined well in the report.
- If the Class D controller had been alert to the pilot reading back something that wasn't intended to be a clearance it might have avoided the accident. That should be as big a red flag as an incorrect read back.
- If the Class D controller had been more specific about the clearance that was available, e.g. Woolgoolga - Bundagen Head at or below 1000 instead of just "at or below 1000 feet" the pilot might not have descended on track.
They weren't the only causes. But they seem significant enough to rate some examination.