I have the same issue. I paid my estimated Underpayment penalties on 4/5/2024 when I filed my Extension. I now can't backdate my payment. If I leave the date of payment blank which implies I paid on 4/15/2024, it shows I owe $28 due to the additional interest for 10 days.
I am thinking that I could just pay the additional $28 and hope that IRS would automatically re-calculate the underpayment penalty correctly. I am assuming IRS would re-calculate since line 38 (penalty) on 1040 is an "Estimate". Worst case scenario is that I overpay $28 which is okay with me as long as I don't owe anything that I shouldn't.
Ideally, I still want the Tax Return to be correct rather than working around the problem. @RyanK @CycloneB what did you guys end up doing? Any insight would be much appreciated.