Great question,

it has been asked on https://github.com/hashicorp/vault-plugin-auth-kubernetes/issues/19

So give a path to your backend

$vault auth enable --path="kube-cluster-A" kubernetes

$vault auth enable --path="kube-cluster-B" kubernetes

vault write auth/kube-cluster-A/config kubernetes_host=HOSTA:8443 ....

vault write auth/kube-cluster-B/config kubernetes_host=HOSTB:8443 ...