It's just the way that it is accounted within the 1040 tax form. Remember that this tax penalty is a separate calculation and shown on the return on a different line than the taxes calculated on the return and included in the taxes due on income line (tax liability). You can think of it this way: The 25% regular tax part is calculated as a part of the regular taxes due line on the 1040 form and the 10% early distribution penalty is shown on the other line as the tax penalty. Your total withholding that you entered into the tax return that is only shown as a total amount on the 1040 form return includes the amounts that help cover both of those instead of separating it into sections.
