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EKS Engineer here.

Calico policy can be used with the AWS VPC CNI, but you can remove the default CNI and install Calico or any other CNI plugin you’d like.

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In theory, you could replace the CNI on worker nodes, but is that something that is practically useful (when it can't be done on master nodes in EKS) and supported? How would the kube-apiserver, for example, communicate to the metrics-server if it is not connected to the Calico network?

You are correct that the API server is only aware of the VPC network, and not any overlays. One solution to the metrics-server or other webhooks is to use host-networking mode so the API server can have connectivity.

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