It seems to me that the notifications you set up on the alert level should be either moved to or made available to set at the alert group level. Or maybe there is a better way to do this, but my understanding of the current options are that it's sort of backward.
For instance, we have setup the Instance Availability alert. We have an alert group for our non-prod oracle databases and one for our production oracle databases. The alert groups setup the grouping of databases and alerts. Then you go into the alert itself to define who gets notified if the alert triggers. Here's the disconnect, without setting up another special instance availability alert I can not setup a different email or notification group to send the alert to for an individual database.
We have one or two databases that specific groups of users want to know if they go down. They don't care to know about everything else. The only way i currently see to do this is by setting up redundantly alerts. If you could create an alert group with a notification option, then you would only need to create the one alert and add groups to it.