Unless the calculation is overridden by the user the program will and does calculate an estimated penalty based on the info the user entered however the fed/state have the right to calculate the penalty based off the info they have on file and adjust the amount reported either up or down and bill you for the balance due or refund any excess paid. I have seen it both ways. For instance the program calculates the penalty based off the date of payment being 4/18 however if you pay the balance due 2/1 then the penalty was too high and the IRS sends a refund. Same thing in reverse ... say the taxpayer says they paid all of the annual estimates in June of 2022 but they really didn't pay until Dec of 2022 then the program's calcuated penalty would be too low.
