I think you are saying that you failed to enter this Form 1099-R before filing your tax return. If so, the amount did not appear on Form 1040 line 5a as required along with being excluded from the amount reported on line 5b, which is what triggered the CP2000.
This would explain the request to file an amended tax return. However, column B of the Form 1040-X will be all zeros and then only "new" information that the Form 1040-X would provide would be your explanation statement that you originally failed to include the distribution on Form 1040 line 5a and show it as nontaxable on line 5b. (Given that you will just be repeating the explanation that you've already provided, I suspect that either you received automated responses or whoever has examined this at the IRS was inadequately trained to be able to interpret the Form 1099-R as representing nontaxable income.)
An early-distribution penalty only applies to the taxable amount of a distribution. With this distribution being nontaxable, this distribution is not subject to an early-distribution penalty.
