There is no specific penalty for non-filing or belated filing of ITC-04 and hence the Suptt. has chosen to levy general penalty u/s. 125 (max amt being 25k X 2 per year). If the amount of levy is insignificant it would be better to buy peace by paying up. Else, the demand can be contested for a lesser value considering that ITC-04 has no revenue implications on the department.
Also, to be practical, GST audit u/s. 65 is like unsheathing of the sword. Dept has to see blood for the sword to be sheathed back. The Suptt whosoever came for audit has to show some revenue collection, else, he would stand scrutiny before the GCM (group committee meeting of ACs). As there was no other adverse findings he has very conveniently chosen Sec. 125.
If the Suptt has charged the maximum penalty please consider filing an Appeal with FAA. You may take a call based purely on the quantum of penalty.
Thanks