So, I did some more troubleshooting, and I believe this has to do with the Bluetooth stack in the Uconnect 3 (2017 models).
The following applies to all of Apple Maps, Google Maps, and Waze unless specifically mentioned otherwise.
- If I turn off Bluetooth and connect the phone to the system via AUX cable, everything works as expected, which means it must be related to Bluetooth.
- If I'm playing music and have the navigation on, there is NO problem: it lowers the music volume, plays the navigation command, the resumes the music volume.
- If it's a podcast and I have it set to "Pause Spoken Audio" it has this issue (it pause the audio, then no sound, then resumes the audio).
- If I uncheck "Pause Spoken Audio" it will treat it like music, lower the volume, play the command, then resume original volume.
- If there is NO audio playing from my phone, but the Uconnect Media is set to BT audio, it will NOT play navigation commands.
- I also tested this in our 2nd car, a 2011 Ford Focus and these issues did not present; everything worked as expected.
This leads me to believe that the Bluetooth "Pause" command that the Uconnect 3 is sending to the phone is not merely telling the iPhone to pause, but also to mute. Since this does not occur in my Ford Focus Sync BT system, it is presumably related to the Bluetooth Stack of the Uconnect 3 system.
For Uconnect 4 (2018+ models), I would wager that this issue doesn't exist as those units have Apple CarPlay.
As such there does not seem to be a way to resolve this problem, and likely never will be. The best options are one of a few workarounds:
- Turn off audio voice commands on your app. If the app isn't trying to tell you anything and you're content to just periodically glance at the map on your own, this works with no interruption to whatever audio (or no audio) you're playing. For those want it, however, this is obviously a non-starter. (Truth be told, I have my audio commands muted 90% of the time anyway. The reason I spent so long trying to solve this problem is that my wife is the primary driver of the van.)
- Play commands over phone speaker. (NOTE: This solution ONLY works for Google Maps and NOT Waze. Apple Maps does not have this option.) While a bit inelegant, this may be the most straightforward solution. Whether listening to music or a podcast, it will pause the BT audio, then play the voice command over the phone speaker. The biggest problem with this solution is that I found it works for Google Maps, but NOT Waze. Interestingly, when I had Waze selected to use the phone speaker, but then played music, it lowered the music volume, played the command over BT, then resumed the original volume. This could be a bug with Waze.
- If equipped, you could choose to use the vehicle's pre-installed NAV for navigation. This would presumably get around this bug, but often Google Maps and Waze are better, faster, more fully featured, and easier to use than the built-in NAV.
- In your navigation app, uncheck "Pause spoken audio" so that the navigation command will play over your podcast. You lose a few words if you were paying attention, but for some this may be an acceptable workaround. It's worth noting however, that this workaround only works if you are actively playing something (music or a podcast). If you were playing nothing, or had manually paused it yourself it will NOT work, which does make this only a sometimes solution, and kind of poor.
- Connect the phone via AUX cable. This will solve the problem to make it work as expected, but also kind of defeats the purpose of having Bluetooth. Even further, thanks to Apple and their infinite wisdom of eliminating the 3.5mm audio jack, it will require an adapter dongle and you cannot charge the phone and use the audio jack simultaneously unless you buy a different charge + audio adapter, which then has not one but TWO wires hanging down from your phone in front of your console.
- Switch to an Android phone the next time you upgrade? (Actually, I'm not even sure that this will work. I've been assuming this is an iPhone specific issue, but it's conceivable that it's not.)
Edit: So when I plug my phone in to the Uconnect USB port I have the same problem, mute when pausing. So to recap: USB, BT - problem, AUX jack- no problem. It apparently is not specifically a BT Uconnect problem. It appears that this is somehow related to the iPhone's external audio integration stack. What's interesting, though, is why this would occur on some vehicles (Pacifica) and not others (my Ford Focus). Further, in searching I did find other netizens who had this problem first appear in their vehicles (not Pacificas) in 2016 specifically with the update to iOS 10 from iOS 9. In any case, the fact remains that there doesn't appear to be a solution, and the workarounds above are the best bet. It does, however, increase the likelihood that workaround #6 (Android phone) may work.