All the federal taxes withheld and reported on the Form 1099-R in box 4 are entered on your tax return as a tax payment (just like from a W-2).
The 10% early withdrawal penalty is only calculated on a tax return and entered as a tax liability. The taxable amount withdrawn is added to your tax return as ordinary income.
If your total tax liabilities are less than your total tax payments you will get a tax refund for the overpayment. If the total tax liabilities are greater than your total tax payments you will have taxes owed.