No, you do not have to pay the 6% penalty since you are removing the excess contribution plus earnings before the extended due date. Make sure you enter the excess contribution amount as removed on the penalty screen at the end of the IRA contribution interview.
You might want to file the extensions if you plan to avoid amending the 2023 return. You will need to know how much earnings were returned with the excess contribution if you want to enter the 2024 Form 1099-R on your 2023 return.
Please see How do I file an IRS tax extension?
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