I have the same problem.
And nobody at Waze or Android Auto understands how it is frustrating.
It should be possible to use android auto without Waze.

I'm having the same issue. I use Waze to navigate to a destination. When I'm done and don't need Waze on my vehicle screen using Android Auto, I want to shut down Waze via Android Auto. I can't physically have my phone in my hand while driving to shut Waze off on my phone.

If you don't want to use Waze, in your car, choose google maps instead. You could also use your phone settings. Search for connected devices, tap android auto, customize launcher, and disable Waze.