You should disable immediately App app, auto-update feature and all connections to GOS servers like time sync, supl, connectivity-checks.

Connections to GOS servers can fingerptint you.

The best you can do is uninstall GrapheneOS. They don't care about your privacy probably on purpose.

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All of the GrapheneOS default connections are thoroughly documented here: https://grapheneos.org/faq#default-connections

The purpose for each is clearly defined, and people are allowed an option to use the standard versions (for example Google servers for connectivity check) where applicable, or the option of disabling them entirely.

Non-default connections that rely on configuration are also documented here: https://grapheneos.org/faq#other-connections

Furthermore, using Tor or a VPN obscures the network the user connects to from seeing connections made to GrapheneOS (if the user chose to allow them). While the connectivity check can't go over a VPN on any OS, that's why the option to turn it off is there.

Automatic updates are highly recommended, but one can disable the built-in updater and sideload updates manually if they so choose, same goes for app updates. This is all documented here: https://grapheneos.org/usage#updates