Thanks for the clarification Mik,

This is indeed a very handy feature, perhaps not too well known and or documented.

What's more, it is quite easy to replace this email by a message. This needs 3 things:

1. Add a messages.php file to the /db directory as a message provider,

2. Add the appropriate string in the /lang/en for this message name

3. Finally, in the /send_email.php file replace 

email_to_user($abouttosenduser, $USER, $data->subject, format_text($data->content['text']), $data->content['text']);

with something like this:

                       $message->component = 'block_configurable_reports';

        $message->name = 'messagefromschool';

        $message->userfrom = $USER;

        $message->userto = $abouttosenduser;

        $message->subject = $data->subject;

        $message->fullmessage = $data->content['text'];

                        $message->fullmessageformat = FORMAT_HTML;

        $message->fullmessagehtml = format_text($data->content['text']);

                        $message->smallmessage = 'small message';

        $message->courseid = $data->courseid;

        $message->replyto = "noreply@example.edu";

      $messageid = message_send($message);

Now this will show up as a notification and obey the user preferences.