"but without a form 8915-E filed for 2020"

Here:

https://proconnect.intuit.com/community/form-1099-r/help/how-to-enter-coronavirus-related-retirement...

Of course you will mark that the 1099-R is a qualified disaster distribution; we've covered this part. Why do you now state "without" that form? You are overthinking this.

"But specifically, what would be amended?"

The 1040X is prepared for the reality you need to report. Not for what should have been that also no longer applies.

"It is only a valid rollover if it was a disaster rollover since it took two years to pay it back. No timely election was made to have it show up in a single year (2020) therefore the income has to be spread over three years."

Moot.

"There is only one way that I know if to do this - 2020 Form 8915-E. Are you suggesting another way?"

No, but you seem to be.

"Since there was unreported withholding"

Oh; that's yet another new piece of information. How can someone forget to include they prepaid $10,000; and withholding typically is 20% of the distribution.

Again, you really are completely overthinking all of this. Follow the instructions.