I have set my templateVM's to update over Tor. Even when sys-whonix isn't running, the update Widget shows that there are new updates, so that must mean it checks over clearnet? I think I've also seen this with R3.2, when Qubes Manager showed the updates icon even though there was no sys-whonix running. There should be a warning on installation when enabling updates over Tor that it still checks over clearnet, or the checking should be disabled by default when the user enables updates over Tor. It would also be nice to have a warning in the Updates section in Global Settings in Qube Manager.
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