If you didn't skip that section AND you owed $1000 or more than the option to let the program estimate the penalty, skip that penalty section altogether or complete the Annualized Income option would have been presented. Once again the program can only compute the penalty if you let it and using the info you provide.
Now the taxing authority computes the penalty using the info they have gathered which may be different than what you listed. For instance the dates you paid estimated payments if any.
