The penalty is calculating relative to the payment cycles. Not to Tax reporting, form due dates, etc. That's why we see this instruction:

"Penalty figured separately for each required payment.

The penalty is figured separately for each installment due date. Therefore, you may owe the penalty for an earlier due date even if you paid enough tax later to make up the underpayment. This is true even if you’re due a refund when you file your tax return. However, you may be able to reduce or eliminate the penalty by using the annualized income installment method."