There are multiple parts to the 2210. Yes, line 6 says don't include estimated taxes paid.
However, you may be able to reduce or eliminate the underpayment penalty by using the Regular Method (Part IV) to compare your withholding plus estimated tax payment against the annualized income.
So in the underpayment interview, ask to try to annualize your income to see if this will reduce or eliminate the penalty.
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