Currently, GFCommon::send_email() is a private method and probably rightly so. However, there is no real way to modify the message contents without re-writing this method. Just something to re-considered because I am betting this was made private on purpose to prevent plugins, etc., from using this method.
However, I believe it would be advantageous to add a filter to the message though I am not sure which would be better, pre-replace_variables() or post. However, I do think that message could benefit from its own method. Something like this:
public static function build_message( $form, $lead ){
$message_format = apply_filters("gform_notification_format_{$form["id"]}", apply_filters("gform_notification_format", "html", "admin", $form, $lead), "admin", $form, $lead);
$message = GFCommon::replace_variables(rgget("message", $form["notification"]), $form, $lead, false, false, !rgget("disableAutoformat", $form["notification"]), $message_format);
$message = do_shortcode($message);
return apply_filters("gform_message_{$form["id"]}", apply_filters("gform_message", "html", "admin", $message), "admin", $message);
}This could replace 2 chunks in send_user_notification() & send_admin_notification() methods. This would also allow someone to hit gform_entry_created and make the necessary changes to the message based on the submission.