When I flag an answer as "not an answer", if it should be a comment, I instead flag it as "other" and put in the box the post that it should be a comment on. When moderating on SQA, I know I wish I could have that feature, and I can only assume that the moderators on SO appreciate the time saver (particularly on questions where there's a lot of answers).
Now, it could be the benefit gained from this box is outweighed by how much the box detracts from the 'elegance' of the menu. I certainly don't want to get in the habit of cluttering up an interface with every possible feature.
So I suppose this is part support, part feature request.
When you identify that something should be a comment, is it really appropriate to have done so without also (as part of the analysis) identify what post the errant post should be a comment on? Assuming that it's not, is it then appropriate to use the 'other' box as a mechanism by which to send the attending moderator the appropriate post id to receive the errant post as a comment?
If it is appropriate to use the other box, then there's nothing to be done. But this might have an impact on your reporting by underestimating the number of errant questions flagged as should be comment (although I suppose the analysis could instead be run on number of questions actually converted, but that only reports actual moderator activity, not community feedback and the effectiveness of said feedback.)
If it is not appropriate, then I suggest a box be added (perhaps it would only appear if 'not an answer' was selected) for entering the post id that should receive the errant question as a comment.