Tom
I don't have a solution for you, but a couple of observations I've made over the years. I think the problem you are describing is either device dependant or Android version dependant. Probably the latter.
When I was using a Motorola Droid X, first on Froyo, then later on Gingerbread, all notifications would come only from the phone speaker. My Bluetooth would only pick up media and phone calls. Ever since I am using a Samsung Galaxy S3, first on Ice Cream Sandwich, now on Jellybean, my Bluetooth picks up notifications as well as phone and media. I suspect this is due to Android combining ringer and notification since ICS.
If I am correct, then your only solution would be to drop back to at least Gingerbread, or switch to a custom ROM that has altered this behavior. Or convince Google they screwed up and get them to change it back.
Scott
Matt
Matt