It's generally up to the plan administrator to determine if the distribution qualifies for NUA treatment. If so, the Form 1099-R will be prepared as you indicated (along with code 1, 2 or 7 in box 7 and the IRA/SEP/SIMPLE box unmarked). Entering such a Form 1099-R (making sure to indicate that you did not move the money to another retirement account but instead "did something else with it") does cause TurboTax to include in taxable income only the amount from box 2a, not the entire gross amount.
