I usually do not have the phone set as the source in the Media Player. I have the radio, TuneIn, or Slacker and the phone does a Bluetooth interrupt to play the alert (or directions if I have that turned on in the Waze app). From the car's perspective, it looks like I'm on a 2-second Bluetooth phone call as I get the usual IC display to "End Call" and a call timer while the alert is playing. Waze does this interruption about 80% of the time. It was 100% of the time, but its hasn't worked as well since they revamped the UI. I suspect they changed part of the code for sounds and that negatively affected this.
When I make the phone the Media Source, I get 100% of the Waze alerts (or directions). Waze reduces the volume temporarily of whatever is playing over Bluetooth from my phone and speaks over the music.