CRA indicates that late filing a financial institution return is not particularly relevant to the imposition of an ETA s. 284.1 penalty

When asked about the application of the ETA s. 284.1 penalty to an unfiled return for a financial institution (on form GST111 or RC7219), and whether a zero dollar line item triggers a minimum penalty amount of $1,000, CRA stated:

Where an information return that was not filed on time is subsequently filed, and the correct amount reported on the particular line is zero … there would be no penalty under subsection 284.1(1) based on the formula for calculation the penalty in that subsection. …

However, CRA went on to indicate (respecting the penalty under s. 284.1(2)) that:

Where a return has not been filed, the CRA may apply the $1,000 penalty for a particular line in the absence of information that would support a lower penalty amount.

Neal Armstrong. Summaries of May 2019 CPA Alberta CRA Roundtable, GST Session – Q.6 under ETA s. 284.1(2) and s. 284.1(3).