As I understand it, the after-tax portion was rolled over to a Roth IRA, the earnings on the after-tax funds while in the 401(k) were rolled over to a traditional IRA and there were no gains (or perhaps there was a loss) on the funds while in the traditional and Roth IRAs.
I think that the employer will only pay to you the amount of the after-tax contribution reclaimed, not the attributable gains, so the gains will be taxable to the employer, not to you. You'll need to verify that with your employer.
Assuming that you timely filed your 2021 tax return, you are correct that removing the excess contributions by 10/17/2022 avoids the 6% excess-contribution penalty for 2021. There is probably no reason to amend your 2021 tax return which would do nothing more than provide an explanation of what happened. Just be sure to retain sufficient records to be able to provide explanation to the IRS if they question the returns of contributions. If they ask for an explanation, the explanation will need to mention that the returns of contributions were obtained pursuant to section 301.9100-2 to indicate that you timely filed your 2021 tax return and that you received the corrective distribution by 10/17/2022.
