You're absolutely right in your reasoning for using custom Notifications. In Flash, you're forced to extend Event if you want a payload, and knowing that some people really don't like having to create the extra classes, I felt it was the right thing to have the base Notification class have a Object payload, but support subclassing if you want to.
As for where to put them, I believe that adding the Notifications at the same level as ApplicationFacade makes the most sense. They have to live somewhere, nothing else is expected at that level, and they are potentially shared by all 3 tiers. That was the reasoning for putting the ApplicationFacade there.
Adding another branch at the MVC level is not really advised. The Cairngorm package structure forces only 2 more folders on you at the MVC level, but every time I find myself at that folder level in a drill down, I find I have to stop and think. Only for a second, but it adds up.
See this related discussion:http://forums.puremvc.org/index.php?topic=8.0-=Cliff>