diff --git a/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/certmanager/certificate.go b/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/certmanager/certificate.go
index fc449472db2..70f4192219b 100644
--- a/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/certmanager/certificate.go
+++ b/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/certmanager/certificate.go
@@ -60,10 +60,10 @@ metadata:
   name: serving-cert  # this name should match the one appeared in kustomizeconfig.yaml
   namespace: system
 spec:
-  # $(SERVICE_NAME) and $(SERVICE_NAMESPACE) will be substituted by kustomize
+  # SERVICE_NAME and SERVICE_NAMESPACE will be substituted by kustomize
   dnsNames:
-  - $(SERVICE_NAME).$(SERVICE_NAMESPACE).svc
-  - $(SERVICE_NAME).$(SERVICE_NAMESPACE).svc.cluster.local
+  - SERVICE_NAME.SERVICE_NAMESPACE.svc
+  - SERVICE_NAME.SERVICE_NAMESPACE.svc.cluster.local
   issuerRef:
     kind: Issuer
     name: selfsigned-issuer
diff --git a/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/crd/patches/enablecainjection_patch.go b/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/crd/patches/enablecainjection_patch.go
index 042f2228add..702a8ef5c24 100644
--- a/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/crd/patches/enablecainjection_patch.go
+++ b/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/crd/patches/enablecainjection_patch.go
@@ -56,6 +56,6 @@ apiVersion: apiextensions.k8s.io/{{ .Resource.API.CRDVersion }}
 kind: CustomResourceDefinition
 metadata:
   annotations:
-    cert-manager.io/inject-ca-from: $(CERTIFICATE_NAMESPACE)/$(CERTIFICATE_NAME)
+    cert-manager.io/inject-ca-from: CERTIFICATE_NAMESPACE_PLACEHOLDER/CERTIFICATE_NAME_PLACEHOLDER
   name: {{ .Resource.Plural }}.{{ .Resource.QualifiedGroup }}
 `
diff --git a/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/kdefault/enablecainection_patch.go b/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/kdefault/enablecainection_patch.go
index d93780f7dfa..a0b3c1d3c56 100644
--- a/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/kdefault/enablecainection_patch.go
+++ b/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/kdefault/enablecainection_patch.go
@@ -45,18 +45,18 @@ func (f *WebhookCAInjectionPatch) SetTemplateDefaults() error {
 }
 
 const injectCAPatchTemplate = `# This patch add annotation to admission webhook config and
-# the variables $(CERTIFICATE_NAMESPACE) and $(CERTIFICATE_NAME) will be substituted by kustomize.
+# CERTIFICATE_NAMESPACE_PLACEHOLDER and CERTIFICATE_NAME_PLACEHOLDER will be substituted by kustomize
 apiVersion: admissionregistration.k8s.io/{{ .Resource.Webhooks.WebhookVersion }}
 kind: MutatingWebhookConfiguration
 metadata:
   name: mutating-webhook-configuration
   annotations:
-    cert-manager.io/inject-ca-from: $(CERTIFICATE_NAMESPACE)/$(CERTIFICATE_NAME)
+    cert-manager.io/inject-ca-from: CERTIFICATE_NAMESPACE_PLACEHOLDER/CERTIFICATE_NAME_PLACEHOLDER
 ---
 apiVersion: admissionregistration.k8s.io/{{ .Resource.Webhooks.WebhookVersion }}
 kind: ValidatingWebhookConfiguration
 metadata:
   name: validating-webhook-configuration
   annotations:
-    cert-manager.io/inject-ca-from: $(CERTIFICATE_NAMESPACE)/$(CERTIFICATE_NAME)
+    cert-manager.io/inject-ca-from: CERTIFICATE_NAMESPACE_PLACEHOLDER/CERTIFICATE_NAME_PLACEHOLDER
 `
diff --git a/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/kdefault/kustomization.go b/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/kdefault/kustomization.go
index 2f3032f7045..0f8dbe2696e 100644
--- a/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/kdefault/kustomization.go
+++ b/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/kdefault/kustomization.go
@@ -55,10 +55,12 @@ namespace: {{ .ProjectName }}-system
 namePrefix: {{ .ProjectName }}-
 
 # Labels to add to all resources and selectors.
-#commonLabels:
-#  someName: someValue
+#labels:
+#- includeSelectors: true
+#  pairs:
+#    someName: someValue
 
-bases:
+resources:
 - ../crd
 - ../rbac
 - ../manager
diff --git a/testdata/project-v3-with-kustomize-v2/config/certmanager/certificate.yaml b/testdata/project-v3-with-kustomize-v2/config/certmanager/certificate.yaml
index 52d866183c7..7301f1bf7b3 100644
--- a/testdata/project-v3-with-kustomize-v2/config/certmanager/certificate.yaml
+++ b/testdata/project-v3-with-kustomize-v2/config/certmanager/certificate.yaml
@@ -15,10 +15,10 @@ metadata:
   name: serving-cert  # this name should match the one appeared in kustomizeconfig.yaml
   namespace: system
 spec:
-  # $(SERVICE_NAME) and $(SERVICE_NAMESPACE) will be substituted by kustomize
+  # SERVICE_NAME and SERVICE_NAMESPACE will be substituted by kustomize
   dnsNames:
-  - $(SERVICE_NAME).$(SERVICE_NAMESPACE).svc
-  - $(SERVICE_NAME).$(SERVICE_NAMESPACE).svc.cluster.local
+  - SERVICE_NAME.SERVICE_NAMESPACE.svc
+  - SERVICE_NAME.SERVICE_NAMESPACE.svc.cluster.local
   issuerRef:
     kind: Issuer
     name: selfsigned-issuer
diff --git a/testdata/project-v3-with-kustomize-v2/config/crd/patches/cainjection_in_admirals.yaml b/testdata/project-v3-with-kustomize-v2/config/crd/patches/cainjection_in_admirals.yaml
index ba7fea6e88d..1d2873a419f 100644
--- a/testdata/project-v3-with-kustomize-v2/config/crd/patches/cainjection_in_admirals.yaml
+++ b/testdata/project-v3-with-kustomize-v2/config/crd/patches/cainjection_in_admirals.yaml
@@ -3,5 +3,5 @@ apiVersion: apiextensions.k8s.io/v1
 kind: CustomResourceDefinition
 metadata:
   annotations:
-    cert-manager.io/inject-ca-from: $(CERTIFICATE_NAMESPACE)/$(CERTIFICATE_NAME)
+    cert-manager.io/inject-ca-from: CERTIFICATE_NAMESPACE_PLACEHOLDER/CERTIFICATE_NAME_PLACEHOLDER
   name: admirals.crew.testproject.org
diff --git a/testdata/project-v3-with-kustomize-v2/config/crd/patches/cainjection_in_captains.yaml b/testdata/project-v3-with-kustomize-v2/config/crd/patches/cainjection_in_captains.yaml
index 9c9d61b0c97..3d3663450e3 100644
--- a/testdata/project-v3-with-kustomize-v2/config/crd/patches/cainjection_in_captains.yaml
+++ b/testdata/project-v3-with-kustomize-v2/config/crd/patches/cainjection_in_captains.yaml
@@ -3,5 +3,5 @@ apiVersion: apiextensions.k8s.io/v1
 kind: CustomResourceDefinition
 metadata:
   annotations:
-    cert-manager.io/inject-ca-from: $(CERTIFICATE_NAMESPACE)/$(CERTIFICATE_NAME)
+    cert-manager.io/inject-ca-from: CERTIFICATE_NAMESPACE_PLACEHOLDER/CERTIFICATE_NAME_PLACEHOLDER
   name: captains.crew.testproject.org
diff --git a/testdata/project-v3-with-kustomize-v2/config/crd/patches/cainjection_in_firstmates.yaml b/testdata/project-v3-with-kustomize-v2/config/crd/patches/cainjection_in_firstmates.yaml
index 6849f00fb85..689c235b3d2 100644
--- a/testdata/project-v3-with-kustomize-v2/config/crd/patches/cainjection_in_firstmates.yaml
+++ b/testdata/project-v3-with-kustomize-v2/config/crd/patches/cainjection_in_firstmates.yaml
@@ -3,5 +3,5 @@ apiVersion: apiextensions.k8s.io/v1
 kind: CustomResourceDefinition
 metadata:
   annotations:
-    cert-manager.io/inject-ca-from: $(CERTIFICATE_NAMESPACE)/$(CERTIFICATE_NAME)
+    cert-manager.io/inject-ca-from: CERTIFICATE_NAMESPACE_PLACEHOLDER/CERTIFICATE_NAME_PLACEHOLDER
   name: firstmates.crew.testproject.org
diff --git a/testdata/project-v3-with-kustomize-v2/config/default/kustomization.yaml b/testdata/project-v3-with-kustomize-v2/config/default/kustomization.yaml
index 64e0ed85302..191ef99df5d 100644
--- a/testdata/project-v3-with-kustomize-v2/config/default/kustomization.yaml
+++ b/testdata/project-v3-with-kustomize-v2/config/default/kustomization.yaml
@@ -9,10 +9,12 @@ namespace: project-v3-with-kustomize-v2-system
 namePrefix: project-v3-with-kustomize-v2-
 
 # Labels to add to all resources and selectors.
-#commonLabels:
-#  someName: someValue
+#labels:
+#- includeSelectors: true
+#  pairs:
+#    someName: someValue
 
-bases:
+resources:
 - ../crd
 - ../rbac
 - ../manager
diff --git a/testdata/project-v3-with-kustomize-v2/config/default/webhookcainjection_patch.yaml b/testdata/project-v3-with-kustomize-v2/config/default/webhookcainjection_patch.yaml
index 02ab515d428..f3dd3f57093 100644
--- a/testdata/project-v3-with-kustomize-v2/config/default/webhookcainjection_patch.yaml
+++ b/testdata/project-v3-with-kustomize-v2/config/default/webhookcainjection_patch.yaml
@@ -1,15 +1,15 @@
 # This patch add annotation to admission webhook config and
-# the variables $(CERTIFICATE_NAMESPACE) and $(CERTIFICATE_NAME) will be substituted by kustomize.
+# CERTIFICATE_NAMESPACE_PLACEHOLDER and CERTIFICATE_NAME_PLACEHOLDER will be substituted by kustomize
 apiVersion: admissionregistration.k8s.io/v1
 kind: MutatingWebhookConfiguration
 metadata:
   name: mutating-webhook-configuration
   annotations:
-    cert-manager.io/inject-ca-from: $(CERTIFICATE_NAMESPACE)/$(CERTIFICATE_NAME)
+    cert-manager.io/inject-ca-from: CERTIFICATE_NAMESPACE_PLACEHOLDER/CERTIFICATE_NAME_PLACEHOLDER
 ---
 apiVersion: admissionregistration.k8s.io/v1
 kind: ValidatingWebhookConfiguration
 metadata:
   name: validating-webhook-configuration
   annotations:
-    cert-manager.io/inject-ca-from: $(CERTIFICATE_NAMESPACE)/$(CERTIFICATE_NAME)
+    cert-manager.io/inject-ca-from: CERTIFICATE_NAMESPACE_PLACEHOLDER/CERTIFICATE_NAME_PLACEHOLDER