If you have a code "P" in box 7 on the form 1099-R you received in 2020, the description for that entry will say "Excess contributions plus earnings/excess deferrals (and/or earnings) taxable in 2019." So, I believe the earnings should be reported in 2019 by entering a substitute form 1099-R in the amended return for that year.
The form 5329 will be generated automatically once you make the 1099-R entry.
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