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If i was using the below in fleet.yaml then looking at rancher web UI would suggest that all 3 values sections were merged/used at once when only TEST used be used. My clusters name is called local. It has a label "env=test".

targetCustomizations:
- name: dev
  helm:
    values:
      replication: false
  clusterSelector:
    matchLabels:
      env: dev

- name: test
  helm:
    values:
      replicas: 3
  clusterSelector:
    matchLabels:
      env: test

- name: prod
  helm:
    values:
      serviceType: LoadBalancer
      replicas: 3
  clusterSelector:
    matchLabels:
      env: prod