When and how should you clam the total overpayment exemption on your W-2 taxes, estimated tax payments, etc.?
You claim it on a W4 only if you had no tax liability (your income tax was zero) the previous year and do not expect to have a liability in the current year. There is no form to claim exempt from estimated taxes.
This makes no sense.
If you failed to have enough money withheld and the line for estimated tax penalty shows something, change it to zero. Nor, not everyone is eligible. https://www.irs.gov/newsroom/irs-waives-penalty-for-many-whose-tax-withholding-and-estimated-tax-payments-fell-short-in-2018
When you file your income tax return. You show your total income subject to taxes and the amount of taxes you paid. If you've overpaid then you get a refund.