I posted this in the firmware thread. The easiest fix for this common problem is when the Audio source is *not* the bluetooth mediao audio connection, then disconnect just the Bluetooth media connection, but leave the BT phone connection active/connected. This would have the affect of the text and email sounds being routed to the phone's internal speaker until the audio source is set to BT, then they'll be routed through along with the music, so you'd still hear them. But now, the text sounds are still going to the BT output, but the car isn't switched to play those.. so they go nowhere.
The problem is that the Model S keeps the Media Bluetooth profile connected all the time, even when it's not being used.
The reason that Waze and other apps do punch through is that they simulate a phone call on the BT Phone connection, which will interrupt whatever else is playing.
The only drawback would be a very short delay when selecting the BT Audio connection while it re-connects with the phone, but that's a small price to pay to be able to hear all the native sounds when no listening to BT audio.