I had a situation last year where I do believe I should have been penalized for a supposed underpayment of estimated taxes, but TT calculated and included one on my return anyway. Since the IRS can calculate it without having to include it in the return I'd rather they tell me a penalty is warranted instead of TT including it.
At the end of the underpayment penalty section in TurboTax you come to a screen that says "Let the IRS Bill Me Later." That screen has two buttons: "Let the IRS Bill Me Later" and "Pay It Now." If you click "Let the IRS Bill Me Later" the penalty will be removed from your Form 1040 and the IRS will calculate the penalty and send you a bill.
Before you do that, as you go through the underpayment penalty section, read the screens carefully and enter any requested information. The screens describe the conditions that can eliminate the penalty and give you the opportunity to remove it.