I sometimes notice that an example question has a comment that answers it, rather than commenting on the question being a good example.
Is it correct to flag the comment as noise?
Yes, if the intent was to provide an answer to the question, then there would be an option to do so.
My suggestion would be to comment to the poster informing them of this meta after someone with more authority than I either comments I'm correct, or better yet, post an answer.
In terms of the comment to the user, you might say something like:
@answer-poster: These comments are intented to provide feedback on the question, not to answer the question, per Area 51 guidelines; if you disagree, please voice that concern on the meta for Area 51. Otherwise please delete your "answer comment", thanks!
Answers reflect on the question - if a comment indicates that a full answer would be too big for a comment box, that suggests that it's a good question. If the answer is completely trivial to find (e.g. general reference), then that suggests the question is less good.