"But we do not have a 1099-R and it won't be issued until 2023."

That's right, and it will be code P = prior year.

"I have no idea why there is a need to amend. It would not change the bottom line."

Are you still overlooking Taxable Income from the earnings?

"Whether we amend or file 5329 as stand alone to pay that 6% excise tax - it would result in the same outcome either way because we were wrong about the earnings for 2021."

And that is why you would amend.

You seem to think the earnings can be left in the Roth, and left to grow as Roth, which would be tax free, but that's not how this works. Since the basis resulting in the earnings is disallowed, there is no tax free income for those. It's called Net Income Attributable (NIA). If you don't remove it, you report it and pay taxes on it. Every year, until it is removed.

Don't confuse Traditional IRA earnings on a disallowed contribution, and a Roth with earnings on disallowed contribution. We are reviewing Roth, right?

https://www.investopedia.com/net-income-attributable-definition-5223368

"Understanding NIA

When a taxpayer makes an excess IRA contribution, both the allowable contribution and excess contribution generate a gain or sustain a loss. The NIA formula was added to the Internal Revenue Code (IRC) in order to assist taxpayers in assigning a portion of the total gain or loss to the excess contribution. The NIA is added to the excess contribution when the amount is returned to the IRA owner.

If the account gained value during the time the excess contribution was in the account, the NIA calculation is positive. The NIA plus the excess contribution must be withdrawn from the account. If the account lost value during the time the excess contribution was in the account, the NIA calculation is negative. The NIA is subtracted from the excess contribution prior to withdrawing funds from the account."

And: https://www.fool.com/retirement/plans/roth-ira/excess-contribution/

"If you catch your mistake before the tax filing deadline for the year, your best option is to remove the excess before you file your taxes. But hold on, it's not as simple as it sounds. You have to remove your excess contribution and any earnings attributable to that excess contribution."

You would use the 1099-R for 2023 if you missed the withdrawal deadline that allows it to be ignored for 2022:

https://proconnect.intuit.com/support/en-us/help-article/federal-taxes/entering-form-1099-r-proserie...

"Code P advises payees that the earnings are taxable in the year in which the contributions were made. If the Form 1099-R has a distribution code P or code R, the distribution is reported on the tax return for the year immediately preceding the year shown on the Form. Sometimes taxpayers will receive notice from their employers letting them know the transaction and amount in time for it to be reported in the original return, but otherwise, it will have to be amended later."

And they give an example: "If the Form 1099-R  is a year 2022 form, you enter this in 2021."

Maybe it's time to read the IRS Pub:

https://www.irs.gov/publications/p590a#en_US_2021_publink1000231025

"Withdrawal of excess contributions.

For purposes of determining excess contributions, any contribution that is withdrawn on or before the due date (including extensions) for filing your tax return for the year is treated as an amount not contributed. This treatment only applies if any earnings on the contributions are also withdrawn. The earnings are considered earned and received in the year the excess contribution was made."