EKS Addon Additional Configurations for CoreDNS. Do not place CoreDNS to Karpenter Managed Node. https://aws.amazon.com/jp/blogs/containers/amazon-eks-add-ons-advanced-configuration/

eks_addon_configurationvalues_coredns.json

{
  "affinity": {
    "nodeAffinity": {
      "requiredDuringSchedulingIgnoredDuringExecution": {
        "nodeSelectorTerms": [
          {
            "matchExpressions": [
              {
                "key": "karpenter.sh/nodepool",
                "operator": "DoesNotExist"
              },
              {
                "key": "kubernetes.io/os",
                "operator": "In",
                "values": [
                  "linux"
                ]
              },
              {
                "key": "kubernetes.io/arch",
                "operator": "In",
                "values": [
                  "amd64",
                  "arm64"
                ]
              }
            ]
          }
        ]
      }
    },
    "podAntiAffinity": {
      "preferredDuringSchedulingIgnoredDuringExecution": [
        {
          "podAffinityTerm": {
            "labelSelector": {
              "matchExpressions": [
                {
                  "key": "k8s-app",
                  "operator": "In",
                  "values": [
                    "kube-dns"
                  ]
                }
              ]
            },
            "topologyKey": "kubernetes.io/hostname"
          },
          "weight": 100
        }
      ]
    }
  }
}