TurboTax's message about not being subject to "additional taxes" refers to the early-distribution penalty that is avoided on a code-2 distribution.
This sounds like an incorrectly prepared Form 1099-R. A Form 1099-R with code 2 in box 7 and the IRA/SEP/SIMPLE box marked is not permitted to have any amount shown for tax withholding. When the recipient is under age 59½, tax withholding is required to be shown on a separate code-1 Form 1099-R.
If you substituted other funds for the portion withheld for taxes, resulting in all $60,000 reaching the Roth IRA, just report the code-2 Form 1099-R as received and indicate that the entire $60,000 was converted to Roth. Otherwise, request corrected Forms 1099-R from the payer, splitting the amount between code-2 and code-1 Forms 1099-R.
