I mentioned RMDs since I thought that you had a non spouse inherited Roth IRA, so this one must be one that you own?
While they cannot refund withholding, you will recover that when you file if you send a corrected 1099R to the IRS. What they said makes no sense, but if you surrendered the principal for a lifetime annuity flow this distribution is an unexpected benefit if they continue your annuity payments as is, but if they underpaid you to date, that would suggest that your future distributions should also increase somewhat to reflect correction of the prior error going forward.
As for your tax filing, the Form 4852 Inst indicate that you should call the IRS and the IRS will send you the 4852 to complete. I hope the IRS is answering their phone these days, because things are a mess there. Of course, you will probably want to wait a time to see if TIIA gets back to you. If they have a logical explanation, I would appreciate your posting it back here. If they do not provide an explanation, I hope you contact the IRS, because TIIA deserves to be contacted by the IRS for their error.
I think the withholding complicates things, and you will get credit for that, so it will be simpler to concentrate on the Box 2a taxable amount and the Box 7 code and forget the withholding since that will take care of itself.
It is possible that pursuing this properly will take enough time so that you will have to file an extension by 4/15. I do not know what would happen if you just went ahead, downloaded the 4852, and filed without waiting for the IRS.