To my understanding, you will get voice turn by turn directions from your mobile phone ONLY when your head unit is in Bluetooth Mode (as opposed to FM/AM mode, CD mode, Satellite Mode, etc.). So basically, music or navigation turn by turn won't pass through the vehicle speakers unless you are in bluetooth mode.
If you are playing music from your phone, via bluetooth or USB, are you are in bluetooth mode, then that music will "dim" and you will hear the turn by turn above it.
Did you have an aftermarket head unit in your 4runner? very curious about how you had mobile navigation travel through your vehicle speakers while playing music from any source, assuming this was the case.