Stack Exchange software doesn't allow the moderators to insert boilerplate comments. There could be a way to automatically insert them with additional software installed on the browser, but I don't know any.
The only difference between a comment left from a moderator, and a comment left from another user is that users are always notified for comments left from moderators, even if the post is deleted right after the comment has been added. In the case of questions, the notification would not give a useful link to the users, as only 10K users can see a deleted question; for answers, notified users would be able to see the answer for which the comment has been left.
You can add the comment yourself. When a moderator is going to delete the answer, and the user who wrote the answer didn't add any comment, the moderator could add a comment (e.g. "What said from @Clive is correct.") to be sure that user gets a notification of the comments left for the answer.
The new revision system uses boilerplate comments for post for which X users selected the same reason from a dialog box.
When you review low-quality posts, you can click on the delete button.
After you click on it, you can choose a reason from a dialog box.
What reported in that dialog is the comment that will be added.
Users who cannot vote to delete posts will see a "Recommend Deletion" button, but the dialog box that appear is the same.
(The last two screenshots have been taken from Stack Overflow, where I cannot vote to delete posts.)