I believe that in the program the penalty calculation is option, you can skip it and wait and see if the IRS bills you. And in that case, if this is the first time you owed a penalty, you can request a waiver.
https://www.irs.gov/businesses/small-businesses-self-employed/penalty-relief-due-to-first-time-penal...
But as the expert said, you can sometimes owe a penalty if you are under-paid in a quarter even if you catch up later. This can happen if you have a large lump sum income such as selling an investment.
