Your income tax is only calculated on your tax return. Withholding is an estimate. You must enter the 1099-R as-is. Your tax is calculated from your overall income and deductions, and you get credit for the withholding. If you had extra tax taken out, that comes back as a refund. You are never "taxed twice" on retirement income.
The reason Turbotax asks for the amount of your RMD is that there are certain things you can't do with your RMD, like roll it over into another IRA. Asking the question helps the program figure out those other issues, but does not result in new tax.
