This is probably a bit of a twist on things, but personally I’d recommend omitting upgrade-nonroot entirely from the Qubes VMs. The reason for this is because upgrading qubes without using Qubes Update or application of Salt states is strongly recommended against for security reasons. Updates with Qubes Update should be doable without root even when qubes-core-agent-passwordless-root is absent (though I need to test this to be sure), but even if that doesn’t work, upgrade-nonroot should still be avoided on Qubes OS.