Yes. If you do not see the penalty in your 2024 Form 1040, then you must amend your 2024 return.
Correct. You would not have received Form 1099-R for the distribution until the following year (2025).
You enter the amount of your original contribution (from Form 5498) in the Deductions and Credits, Retirement and Investments section.
At that point, the system will alert you of the excess contribution and generate Form 5329, along with penalties (for 2024)
Once you have amended your 2024 return with the above information, you can then work on your 2025 tax return.
You will then enter the Form 1099-R to reflect the removal of the excess contribution, not for penalties. The penalties were calculated with the 2024 amendment.
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