Send Navigation Audio to handset but music to bluetooth
Audio routing would have to be set in the application code itself.

However, direct audio routing is deprecated since API level 5 (Android 2.0).

Older versions of Android Navigation had this direct audio routing set to the ROUTE_SPEAKER in their application code. But the newer versions of Android have a system wide flag set with setSpeakerphoneOn or setBluetoothScoOn if it should use the speaker or bluetooth.

I'm afraid that you won't be able to change anything about your setup since it is all build into the system and application code. All sounds will be routed through the same audio output in the newer versions of Android and Android Navigation.