When closing a question (as a moderator) I leave a comment explaining why, and pointing the OP to the faq, unless this has already been done.
What seems a little odd is when community raises the following flag:
Please explain the nature of this closed question via a comment – Community
Is it just an automated script that doesn't check to see if you have left a comment? If so then I'm happy to ignore it, but wouldn't it be useful if it checked?
This is possibly related to: "Please add a comment explaining.." still shows up when I add a comment and then downvote but is in different circumstances.