Think about it. You're telling the navigation app to stream the audio over bluetooth. It's exactly the same as if you were playing a song. If you have MFT listening to FM then how would it know that it needs to switch to bluetooth? Moreover - how would it know to switch to bluetooth to hear the directions then switch back to FM (or Sirius or CD or USB, etc.)?
The solution is what Google maps is apparently doing where it uses the phone connection because that is designed to interrupt the current audio source.
I expect this would work exactly the same way on all vehicle bluetooth interfaces.