You only pay a penalty to the Tax Man if you try and defraud him. You are justified in your claim, whether or not the ATO agrees. Worst case scenario is that they audit you and reject your claim. Their initial reaction is to charge you the unpaid tax and a penalty. You have the right to appeal and when you put your case forward, the case SWH has made, you will win the appeal. You will then be charged the unpaid tax plus interest at the supposed current rate, probably up to 8% which you could then appeal again. I wouldn't recommend the second appeal.
Your claim is justified, you have spent far more on your qualifications than the average person ever will and the subjects, in all probability, will lead to the ATO getting a much larger slice from you in the future.
I have been charged by the ATO with not paying the correct levy on Medicare and a second time of not declaring dividends. I was penalised, appealed on the basis of them both being honest mistakes and merely had to pay the unpaid tax plus interest.
Make the claim.