If you have an unregistered gun, can you go ahead and register it without penalty?
Yes, but it's a complex process (overly complex) like most of what happens with Australian firearms laws, and also costs more than it needs to (again, common with Australian firearms laws).
You would have to put the weapon into the hands of somebody who is permitted to have unregistered firearms in their possession (generally a gun dealer who would charge you for this). Then you would have to get a 'Permit to Acquire' (which costs you money) for the weapon. Assuming it's a weapon you're licenced to have, it after the PTA is processed, it can be transferred back to you as a registered firearm.
At least that's how it works in my state (Victoria).