Amending filing status to fix Roth overfunding

A married couple lived together the entire year of 2020. Taxpayer’s wages were $90k. Spouse’s wages were $84k. Combined AGI was under $175k, which was comprised of primarily wages plus some small dividends & interest. Taxpayer contributes $6,000 for himself to a 2020 Roth IRA prior to a timely tax filing without extension.

Taxpayer and wife, split their taxes, filing married/separate for a net savings just over $512. The net difference in federal refunds was literally $2, with the bulk net savings coming from the NYS tax returns. The taxpayer’s Roth IRA became technically over-funded for 2021 and 2022 to date, as the Roth should not have been funded with income over $10k when filing married/separate. This exposes the taxpayer to the 6% per annum excise tax on the entire $6,000 IRA contribution, income tax on the IRA earnings, the 10% penalty for early withdrawal as the taxpayer is under age 59 ½, plus interest.

Taxpayer has two or perhaps three options.
1. Do nothing and roll the dice, knowing that the excise tax penalty has no statute of limitation.

2. Take corrective measures to remove the 2020 Roth contributions funded.
Pay the excises taxes, income taxes, penalty and interest.

3. This last option is curious as it is not mentioned in available tax literature and seems so obvious, that my antennae go up…

What if the couple amend the federal and NYS tax returns from Married/Separate to Married/Joint, which is permitted prior to the statute deadline? If filing joint, their combined AGI ( under $175k) would ordinarily permit funding of the taxpayer’s Roth IRA without issue. The cost of this option would theoretically be the extra $512 refund plus interest. And the Roth would perhaps be salvaged.

Does this fix the problem? Or is there a hook that still subjects the taxpayer to the same obligation to remove the Roth IRA funds and attributed earnings, even after amending both spouse’s federal and NYS 2020 tax returns to married/joint?