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