No, the withholdings shown in box 4 will be taken into account on your return just like withholdings reported on a W-2 would be.
The 10% penalty is for taking an early distribution from a retirement account without having a valid exception to claim. This penalty is in addition to the distribution itself being included as part of your taxable income. TurboTax will show you a list of possible exceptions to the early distribution penalty. If any of these apply to your situation, enter the amount that was used for the exception in the box beside the applicable category to reduce your penalty.
To learn more, see the following TurboTax help article:
How does a retirement plan withdrawal (Form 1099-R) affect my taxes?
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