I was hoping that such a notation might be part of the transcript, but I suspect that the transcript simply does not include the notations and the fact that it is not present in the transcript is meaningless. This leaves the possibility of either an inexperienced examiner placing more significance on the difference between the total and the taxable amounts than is warranted, or you just got randomly selected to provide additional documentation. It seems unlikely that the IRS Automated Underreporter System flagged the difference as a discrepancy.
I have not seen any other mention [Edit: this year] of a CP2000 being generated for a QCD.
