A tax return is like a balance sheet. The tax increase attributable to the $28,000.41 distribution is not determined until the distribution is combined with all of the other information on your tax return. The $3,202.08 is simply a prepayment toward the overall tax liability determined on your tax return, just like tax withholding from a W-2. The $3,202.08 appears on your tax return as a credit on line 17 to be subtracted from your overall tax liability, so you aren't paying this amount twice.
