The penalty is on your 2020 income and return. It just looks at your 2019 tax to see if you have an exception to the penalty by paying in as much withholding for 2020 as the tax liability on your 2019 return. Even if you have a refund on your 2020 return you can still owe a penalty for not having enough withholding taken out or by not paying in evenly during the year.
