If you think you could have benefited from having the penalty calculated using the annualized income method, that is another choice you could have made in the Underpayment Penalty questionnaire.
The underpayment penalty (Internal Revenue Code section 6654) is part of the laws that the IRS is charged with administering. TurboTax simply provides users the chance to calculate it before they submit their return.
If you don't show the penalty on your return, then the IRS will calculate it and send you a bill if a penalty is due. If you don't agree with the IRS bill, you have the opportunity to respond to the bill. You could submit another calculation using the annualized income method or submit an explanation.
See this TurboTax tips article and this IRS webpage for more information about Form 2210, Underpayment of Estimated Tax.
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