A quick look at the ATO website reveals the important information that leave owed cannot be included in a VR payment. Also, date of receiving a VR payment effects the resultant net payment. The first (approx) $125K income in that tax year is tax free, every incremental dollar is then taxed at a concessional rate.
Obviously the best outcome would be to get a VR payment on 01/07, and have the maximum allowable fraction of that payment made directly into the pilot's super account. Perhaps an agreed amount could be set aside for a subsequent super contribution 366 days later to sweeten the deal?