I had the same issue on my '17... VERY annoying. As you pointed out, when Car Play doesn't connect, it does not default to BlueTooth... you are just left totally disconnected.
I asked the dealer to look into it when my car was in for the 1200 mile service last week. I assumed they wouldn't be able to replicate the issue, but fortunately, they were. They performed a "Battery and Control Module Reset." I lost some stored settings in iDrive, but Car Play seemed to work with my iPhone 6s (iOs 9.XXX) without any problem on Friday evening. I didn't drive the car all weekend, and this morning synced my new iPhone 7. System performed without issue on the drive to work this morning.
I'll report back if the issue resurfaces...
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