"On the 2023 amended return, can I consider and report the 2023 normal distribution as clearing the excessive contributions, such that I will not need a 2023 Form 5329 & penalty payment?"
Yes.
Your distribution in 2023 actually included a distribution of the excess contributions made for 2021 and 2022, so no excess carried over to 2024.
The distribution that you received in 2025 is therefor unrelated to any excess contribution. If still within the 60 rollover window you could roll that distribution back into an IRA.
Since no calculation of net attributable income on the 2022 excess contribution was done, you'll need to treat the 2023 distribution as correcting the 2022 excess contribution after the due date of the 2022 tax return even though you might have made the distribution before the due date of the 2022 tax return, including extensions.
To accommodate 2023 TurboTax, you'll need to split the 2023 Form 1099-R into two, one reporting a distribution of the combined excess (with no adjustment for investment gains or losses) and the other for the remainder of the distribution. When entering the one for the combined excess, enter a zero in box 2a instead of entering the same amount as is in box 1. This is a special indication to TurboTax that the distribution represents a distribution of excess contribution after the due date of the corresponding tax return so that as you proceed after clicking the Continue button on the page that lists the Forms 1099-R that you have entered, TurboTax will eventually prompt you to prepare the required statement to explain this as a return of the excess contributions. The Form 1099-R for the remainder of the distribution will have the same amount in box 2a as is in box 1. Any tax withholding form this distribution can be split between these two 1099-R forms any way that you wish. 2023 TurboTax will exclude from Form 1040 line 4b the entire combined amount of the excess.
Assuming that you have already begun your 2024 tax return with 2024 TurboTax, you'll simply need to zero out the amount of excess originally carried over from the 2023 tax file.
Note that if your 2021 and 2022 tax returns included Form 8606 to add your excess contributions to basis in nondeductible traditional IRA contributions, unless the TurboTax program has changed from when I last checked, TurboTax fails to later reduce the amount of basis by the the amount of excess contribution distributed after the due date. This means that you'll likely need to adjust the basis yourself, probably in 2024 TurboTax by subtracting the amount of the excess contributions distributed.
