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 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".