Yes it will figure the penalty automatically. It will reduce a refund or add to a tax due. But the amount Turbo Tax calculates (or doesn't) on your return line 38 is only an estimate. Turbo Tax can not figure it accurately because they don't know exactly when the IRS or state will get your return and tax due payment. It's common and normal and expected for the IRS or state to bill you for more or send you a refund.
