I can't guarantee that there is a right way to do this (especially with the IRS in the shape that it's in), but you might try telling TurboTax that you want the IRS to bill you for the underpayment penalty (it's in the interview at Other Tax Situations->Underpayment penalties). Then when the IRS bills you, you'll have someone to reply to and request the abatement.
Otherwise, I am not sure how you will get anyone's attention on this.
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