But, according to the IRS (see here) -
“To the extent an overpayment of the 2020 tax exists as of April 15, 2021 (because payments made on or before April 15, 2021, exceed the 2020 tax liability), and the taxpayer makes a valid election to apply the overpayment to 2021 estimated tax, the overpayment would be applied as of April 15, 2021, whether the 2020 return is filed on April 15, May 17, or October 15, 2021.”
So any amount of your overpayment you apply to 2021 estimated tax on your 2020 tax return, regardless of when the return is filed, is treated as having been received by the IRS by April 15, 2021 – assuming that all the tax payments reported on the tax return were made before April 15, 2021.
So, if you file an extension with a payment of anticipated tax due and when you finally prepare your return you are entitled to a refund this may not apply. But if all the tax payments reported on your return were made via withholding and/or timely paid estimated taxes you are OK.