We were talking about Nav's from Bendigo to Moorabbin being forced to transit OCTA. I then suggested going into Essendon.
Going into Essendon CTA / Class C and landing or not (cheaper if you don't) is far more complex than obtaining a VFR transit from Bendigo to Melb in Class C. There would be far better value to depart Moorabbin for Essendon, depart out to the east and then whatever, than a VFR transit over the top of Melbourne.
Getting knocked back on a clearance in the aforementioned scenario does not sound like grounds for a repeat NAV. The school that I do my AFR's at doesn't even actually mandate entry into CTA to comply; they simply assess you on your ability to set yourself up for it and request the clearance.
If a school forced you to re-do a NAV based on the opening posters scenario, then that school is run by money-hungry low-lifes and the student should find another school.