Think I may have answered my own question, but still keen to hear from others:
From the ATO website. Accounting for GST on a non-cash basis
Sales
You account for the GST payable on the sales you make in the reporting period in which you issue a tax invoice or receive full or part payment, whichever happens first.
This means that if you receive a payment before issuing the tax invoice, you must include the GST amount in the reporting period in which the payment happened, even if it is not the period you issue the invoice
