This is not exactly an answer, but bear with me. Your spouse is no longer eligible for an ITIN because she has an SSN. So if an SSN issued in 2023 isn't allowed for a 2022 Form 1040, how could she file? Answer, your CPA is wrong and she must use her SSN. For something from the IRS to show him/her:
https://www.irs.gov/forms-pubs/using-a-social-security-number-ssn-or-individual-taxpayer-identification-number-itin-when-filing-your-tax-return
While this is not a citation from the Internal Revenue Code, it is quite clear "Once you are issued an SSN, use it to file your tax return".
As for question #2, you just file Form 1040X amended return for 2020 and 2021 to include both of your worldwide incomes, include both of your names/SSNs, check the box for married filing jointly. For sure your CPA knows how to handle this.
The above are my personal opinions. Although I am a tax accountant, I am not giving professional advice.