Hi Newsilverfan,
Before you consider the ATO audit, Each year as you know you will need to have your SMSF audited.
The SMSF auditor will need to be satisfied with the existence and valuation of the precious metals held in the SMSF.
If you are making a purchase, the auditor will review the documentation to support the purchase as well as the the purchase (cash) debited from the bank account. For instance, you can use a bullion provider, the purchase should be in the SMSF name.
In relation to storage other than a safety deposit box, store at a provider such as Perth Mint etc who will provide the details required for an auditor to obtain comfort over valuation and existence. Do not store at home....
At year end - 30 June, and you donot use a storage option, an auditor may inspect the gold to verify existence and valuation OR ask for a sworn statutory declaration of the visit by the members/ trustees to the vault including date and time. In this date and age, members will prove the visit with a simple photo with the gold in the valult on the Iphone

All of the above will satisfy external audit (I need to disclose, i'm a auditor) and pass an ATO audit.
Hope that helps and let me know if you need more info.
Cheers, Ivan