When Turbotax calculates the estimated tax payments for 2025, does it include the overpayment from 2024 that I want applied to 2025 taxes?

No.  But you can enter the amount you plan to apply as one of the payments you already made.

We allocated a portion of our 2024 tax return to be applied against 2025 estimated taxes.  That amount shows on the 1040 but was not carried to the actual calculation.  The "Estimated Tax Payment Options" form didn't grab our applied overpayment and won't let me put that number in. Thus  TurboTax printed 4 estimated vouchers.  Seems that something is wrong in the software as we're having far more 2024 overpayment applied to 2025 than we owe in one estimated tax payment.  This is in the desktop software, FYI.

Can you clarify were you were trying to enter the overpayment?  How is it not letting you enter?  Is the boxes grayed out?