When doing its calculation of the number of days late an estimated tax payment might be, TurboTax uses the payment dates that you enter. However, the IRS seems to apply an undocumented grace period for making estimated tax payments. The result can be that the IRS calculates a lower penalty, resulting in a refund of some of the amount determined by TurboTax's more conservative calculation of the penalty.
By conservatively basing the calculation on the dates that you enter and the IRS-documented due-dates rather than calculating a lower amount using undocumented behavior of the IRS, the chance is minimized that you would receive a bill for an additional penalty that could include additional interest being owed.
Regarding amending your tax return, see page 9 of the instructions for From 1040-X regarding Refund or Amount You Owe: https://www.irs.gov/pub/irs-pdf/i1040x.pdf
