It's a bug. You should contact the author.
A workaround to add a class for skinning would be to create the message as a widget first, add your class and then pass it to Y.Notify:
var message = new Y.Notify.Message({
message: 'Some message',
timeout: 1000
});
message.get('boundingBox').addClass('my-skin-class');
notification.add(message);
Another option would be to add it as an object to the notification widget and then retrieve it using item(index)
:
notification.add({
message: 'Some message',
timeout: 1000
});
notification.item(notification.size() - 1).get('boundingBox').addClass('my-skin-class');