The flag itself doesn't send out any notification.

If the answer is deleted or converted to a comment and the moderator who does that leaves a comment, the user will be notified of that comment.

I typically leave comments on most not-an-answers that I remove if they're recently posted. There's not much point in commenting on something that's over a year old, for example.

You can certainly leave a comment of your own, especially since there may be enough time for the user to see it before a moderator sees your flag. You can use a [handy userscript](https://stackapps.com/questions/2116/autoreviewcomments-pro-forma-comments-for-se) to store and reuse the most common comments. It comes with a few pre-loaded that you can use right away, but I like to edit them to make the language more "mine".