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SUC is just good for changing versions, not for managing configuration.

Is there a tool that is good for both managing configuration & changing versions?

For standalone clusters, just your automation / desired-state-configuration tool of choice. But really this sort of thing is why Rancher exists - to manage provisioning, configuration, and version of many clusters.

Right: But Rancher doesn’t do much RKE2 management on the upstream cluster; I need to build that first, then install Rancher on top of it. Rancher manages downstream clusters well, but I’m trying to figure out Rancher’s intended tools for RKE2 on the upstream cluster.

Rancher does not currently suggest any tools for managing configuration of the local cluster. How you manage the cluster that Rancher is deployed to is up to you to decide, based on what fits your environment best.