While I understand the sentiment behind the comments, especially if they being downvoted as "not a good example", I think that these comments are not particularly useful and detract somewhat from the purpose of the example questions.
The power of voting on the example questions is that people decide for themselves whether they think it is on or off-topic. What the author thinks it is is largely irrelevant, and for that reason I would (in most cases) classify these comments as noise. Not only that, if these comments influence the vote in any way, it detracts from the usefulness of the voting.
I am not completely sure why, but I also feel like I am less likely to vote on example questions that have these comments.
So are these Area 51 comments helpful at all? And if not, can I flag them as noise?