Tax withholding, estimated tax payments and any amount paid with a request for filing extension are applied as credits on your tax return. If these total more than the tax liability calculated on your tax return, you get a refund. That's was a tax return is for, to reconcile the total amount sent to the IRS against the tax liability determined on your tax return.
Tax credits such as the EV tax credit are only applied against income taxes, not any IRA early-distribution penalties or any other taxes that are not income taxes.
