I believe that the Internal Revenue Manual indicates that an automatically detected mismatch flags the Form 1099-R reporting on the tax return for examination by a human. The examiner should then look at the tax return, and, if an appropriate explanation statement was included, it should be present in the IRS-scanned copy for the examiner to take into account. There is a good chance that the examiner will then make the correct determination that there is, in fact, no underreporting of income and will mark the flagged Form 1099-R as having been reported correctly, but examiners are human and humans can make mistakes.
