If you make additional payments before filing, then do follow the instructions to enter them as Additional Payments in TurboTax.
Yes, it's correct that they won't be counted as timely Estimated Payments for 2022, because that deadline has passed, but making the payments now is an option you have to get the payments on record with the IRS and State while you are waiting for the IRS problem to be resolved so that you can e-file.
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