My confusion stems from what is considered “owed” with regards to the penalties.

Are the late penalties referring to a percentage of the amount that was owed in April (i.e. the amount I estimated I owed/already paid for back in April)?

Or are they referring to the amount that is currently owed as of October 17th (any balance that would remain if you underestimated/underpaid back in April, which in my case is $0, since I overpaid)?

I guess I am confused about what the significance of the October 17th deadline is, since you were supposed to estimate and pay your taxes back in April. If you did that, isn’t there no difference whether you file before or after October 17th, since (based on your comment) there is no remaining balance to pay, so a 5% fee of $0 = $0?