The main issue here is that flying under civil regs is done under the Civil Aviation Act, while military ops are under the Defence Act. So its really about covering your butt with legal armour for when your flying draws some crabs. Even though this is practically stupid, it the reality of our current Australian law.
On the other hand, the pragmatic Kiwis have legal recognition of their Military/Civil instrument ratings and they are for all intents and purposes equal. They also utilise the same set of rules. We tried this back in the 90's....but Defence didn't care and the civil lawyers killed it off.