Remember, if a refund is due, no penalty is charged on the late return filed by a taxpayer.

Shop talk:

The above was part of IR-2020-207, but I suspect it was technically wrong. 

The Failure to File penalty is computed based on the underpaid amount as of the original due date.

Say, original due date 4/15.  Extension filed with no payment.  Payment $5,000 made in October.  Return filed in January  (90 days late counting extension)  Refund of $1,000.  Technically, a refund is due on the return, but I believe failure to file penalty is applicable - computed based on $4,000.

@IRonMaN  since i don't know if you also work for the IRS, could you check the above with your colleagues that I don't know whether you have?