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The year of the Linux phone please
This scan will happen on device and only if the phone has google play services installed. I doubt if any custom ROM will be blocking apps from third party stores.
Custom ROMs are in trouble on their own (seems to me Google is engaging in a multi-pronged attack on personal software choice), and some people can’t install a custom ROM.
GrapheneOS says Google’s recent changes will not stop them and it’s nothing to worry about.