This is a known issue with Android Auto itself. It doesn't allow any navigation app to be loaded into AA that wasn't installed by Google Play. Try installing CoMaps via Google Play and it will appear in AA. Only navigation apps are affected by this.
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I am using lineageos with Magisk. I installed the Android 4 Auto MicroG Module and the Android Auto - XLauncher Unlocked. With this i can see almost any app on Android Auto, even of they are not installed from Google PlayStore. I don't know if you can do something similar with GrapheneOs.
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