The IRS will not pay any refund on an amended return filed more than 3 years after the due date, but they will always take an amended return to correct the records (and pay more tax). Because 2021 is past the 3 year statute of limitations (originally due April 2022, expired April 2025), you could think about skipping the 2021 return and just listing the excess as a prior year excess on the 2022 form. This would result in the excess just "appearing" in 2022 without indicating when the excess contribution had been made, but in theory it is too late for the IRS to audit you and assess penalties for 2021 (assuming you originally filed on time). I suggest asking your own tax pro before you decide to skip 2021.
Each form 5329 must be that year's form -- 2021 for 2021, and so on, check the date at the top. Past year forms are here.
https://www.irs.gov/forms-pubs/prior-year
Check the instructions. I believe you are correct that if the only thing you are changing is the penalty, you need the 1040-X and the 5329 but you don't need an entire 1040. But I am not 100% sure since I have not personally experienced this situation.
Mail each amended return separately, not all together.
