You could be forgiven for thinking that the very fact that the taxpayer was estimating the amount of unprocessed invoices would indicate that they couldn’t be certain that those invoices were in their possession at the time the return was submitted, but the reality is they are two very different exercises.
The ATO has now stated that they will 'properly assess the correct net amount based on invoices which can be demonstrated to have been held', and it follows that a discrepancy would result in an assessment to tax plus a charge to interest - the latter could be the more significant amount depending on the time scales involved.
There is nothing wrong with adjusting for input tax on invoices actually received after the end of the accounting period but attributable to an earlier GST return, however if you are or have been using an 'estimator tool' you might want to consider the potential for assessments & interest and look at making a voluntary disclosure. It would also be worthwhile to review what evidence you will be able to produce to verify when you physically received the invoice. Some of these 'tools' have been in use for many years and the exposure to a general interest charge, which is considerably higher than the bank rate (currently 12 percent), could now be quite significant.