You can check the box. It will not cause any issues, since what matters most to the IRS is that the numbers match their records.
If you emptied the account, checking the box accurately reflects the status of the account.
The important thing to look for is Code 4 in Box 7, since it is an inherited IRA.
Are you sure that TurboTax isn't asking if box 2b Taxable amount not determined is marked. For a distribution from an inherited traditional IRA, box 2b Taxable amount not determined should be marked, box 7 should have code 4 and the IRA/SEP/SIMPLE box should be marked. If neither box 2b Taxable amount not determined nor the IRA/SEP/SIMPLE box is not marked, the distribution is not from any type of traditional IRA but is instead a distribution from an employer plan like a 401(k).
If the distribution is from an IRA, the marking (or not) of box 2b Total distribution is irrelevant. It has no bearing on how the IRA distribution is taxed.