If I recall, the 1099R did not have the “IRA” box in line 7 checked, and show the same account # as the Q coded payments. Therefore, this distribution is still being treated as a Roth distribution other than the 7 code. I think your 4852 will make the case that this distribution also should have been coded Q. If so, it would be inconsistent to pay tax on the earnings and they should be treated like the rest of the distribution.
These earnings are not excess amounts in any way. Underpayments to plan participants from prior years typically require earnings to be paid as well, and while I cannot locate any IRS guidance on remediation payments specifically, I don’t know why they would be treated any different than other plan underpayments to participants.