Based upon Notice #20-05, the April 15 due date for my 2019 F&E return has been extended to July 15. If I have an overpayment of tax when I file my 2019 F&E return on July 15, 2020, can it be applied to my 2020 quarterly estimated payments?

Yes, but it will be applied as of July 15, 2020.  The Department extended the due date of the first quarter estimated payment, extension payment and the tax return from April 15, 2020 to July 15, 2020.  The due date of the remaining quarterly estimated payments for 2020 has not changed. For example, the second quarterly payment is still due on June 15, 2020, and should be made on that date regardless of any overpayment that may be computed on the 2019 return.