Kustomization trying to apply wrong version of terraform object

[nab-gha]

I am repeatedly hitting issues with a kustomization that is applying a terraform object. The terraform object is version v1alpha2 but Kustomization intermittently tries to apply it as v1alpha1 causing an error and removing fields that are new in v1alpha2

flux version
flux: v2.0.0-rc.5
helm-controller: v0.34.1
kustomize-controller: v1.0.0-rc.4
notification-controller: v1.0.0-rc.4
source-controller: v1.0.0-rc.5

See https://github.com/ww-gitops/paulcarlton-ww-macbook/blob/main/infra/dynamic/eks-config/eks-config.yaml#L1 for terraform yaml specifying v1alpha2

The kustomization is shown below, this is generated by GitOpsSets

paulc:paulcarlton-ww-macbook paulc [sandbox]$ kubectl get kustomizations.kustomize.toolkit.fluxcd.io -n test-two      test-eks-config-c1      -o yaml
apiVersion: kustomize.toolkit.fluxcd.io/v1
kind: Kustomization
metadata:
  annotations:
    reconcile.fluxcd.io/requestedAt: "2023-06-08T12:05:09.935189+01:00"
    templates.weave.works/create-request: ""
  creationTimestamp: "2023-06-07T09:05:43Z"
  finalizers:
  - finalizers.fluxcd.io
  generation: 1
  labels:
    templates.weave.works/name: test-eks-config
    templates.weave.works/namespace: test-two
  name: test-eks-config-c1
  namespace: test-two
  ownerReferences:
  - apiVersion: templates.weave.works/v1alpha1
    kind: GitOpsSet
    name: test-eks-config
    uid: 83b72996-e275-40c7-be94-73ce81ca27e7
  resourceVersion: "394234"
  uid: 0b905535-275c-4f0c-8f93-7694132ac391
spec:
  dependsOn:
  - name: test-eks-c1
  force: false
  interval: 1m0s
  path: ./infra/dynamic/eks-config
  postBuild:
    substitute:
      clusterName: c1
      desired_size: '"2"'
      resourceName: test
      target_path: clusters/test-two/test/
      templateNamespace: test-two
    substituteFrom:
    - kind: ConfigMap
      name: cluster-config
      optional: false
  prune: true
  sourceRef:
    kind: GitRepository
    name: flux-system
    namespace: flux-system
  timeout: 5m
  wait: true
status:
  conditions:
  - lastTransitionTime: "2023-06-08T11:05:10Z"
    message: Detecting drift for revision main@sha1:1f3037dfe7ef90888acae6b5d6dce8b690d5dac4
      with a timeout of 5m0s
    observedGeneration: 1
    reason: ProgressingWithRetry
    status: "True"
    type: Reconciling
  - lastTransitionTime: "2023-06-08T11:05:10Z"
    message: |
      Terraform/test-two/eks-config-test-c1 dry-run failed, error: failed to prune fields: failed add back owned items: failed to convert merged object at version infra.contrib.fluxcd.io/v1alpha1: .spec.runnerPodTemplate.spec.hostAliases: field not declared in schema
    observedGeneration: 1
    reason: ReconciliationFailed
    status: "False"
    type: Ready
  - lastTransitionTime: "2023-06-08T11:04:38Z"
    message: 'timeout waiting for: [Terraform/test-two/eks-config-test-c1 status:
      ''InProgress'']'
    observedGeneration: 1
    reason: HealthCheckFailed
    status: "False"
    type: Healthy
  inventory:
    entries:
    - id: test-two_eks-config-test-c1_infra.contrib.fluxcd.io_Terraform
      v: v1alpha2
  lastAppliedRevision: main@sha1:55d8d6ac2e5dfba25fc177e904f1ee0bb1db4cdb
  lastAttemptedRevision: main@sha1:1f3037dfe7ef90888acae6b5d6dce8b690d5dac4
  lastHandledReconcileAt: "2023-06-08T12:05:09.935189+01:00"
  observedGeneration: 1