diff --git a/config/certmanager/certificate.yaml b/config/certmanager/certificate.yaml
index c493d05a4..2c93395ae 100644
--- a/config/certmanager/certificate.yaml
+++ b/config/certmanager/certificate.yaml
@@ -12,7 +12,7 @@ spec:
 apiVersion: cert-manager.io/v1
 kind: Certificate
 metadata:
-  name: serving-cert  # this name should match the one appeared in kustomizeconfig.yaml
+  name: serving-cert
   namespace: system
 spec:
   # WEBHOOK_SERVICE_NAME_PLACEHOLDER and WEBHOOK_SERVICE_NAMESPACE_PLACEHOLDER will be substituted by kustomize
diff --git a/config/certmanager/kustomization.yaml b/config/certmanager/kustomization.yaml
index e0182475f..438e93c2c 100644
--- a/config/certmanager/kustomization.yaml
+++ b/config/certmanager/kustomization.yaml
@@ -1,5 +1,6 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
+
 resources:
 - certificate.yaml
 
diff --git a/config/certmanager/kustomizeconfig.yaml b/config/certmanager/kustomizeconfig.yaml
index d6109c9d8..29091b12d 100644
--- a/config/certmanager/kustomizeconfig.yaml
+++ b/config/certmanager/kustomizeconfig.yaml
@@ -1,4 +1,4 @@
-# This configuration is for teaching kustomize how to update name ref and var substitution 
+# nameReference teaches Kustomize which fields represent a resource name.
 nameReference:
 - kind: Issuer
   group: cert-manager.io
@@ -6,14 +6,3 @@ nameReference:
   - kind: Certificate
     group: cert-manager.io
     path: spec/issuerRef/name
-
-varReference:
-- kind: Certificate
-  group: cert-manager.io
-  path: spec/commonName
-- kind: Certificate
-  group: cert-manager.io
-  path: spec/dnsNames
-- kind: Certificate
-  group: cert-manager.io
-  path: spec/secretName
diff --git a/config/crd/kustomizeconfig.yaml b/config/crd/kustomizeconfig.yaml
index 8e2d8d6b1..69dff6de6 100644
--- a/config/crd/kustomizeconfig.yaml
+++ b/config/crd/kustomizeconfig.yaml
@@ -1,4 +1,4 @@
-# This file is for teaching kustomize how to substitute name and namespace reference in CRD
+# nameReference teaches Kustomize which fields represent a resource name.
 nameReference:
 - kind: Service
   version: v1
@@ -7,11 +7,9 @@ nameReference:
     group: apiextensions.k8s.io
     path: spec/conversion/webhook/clientConfig/service/name
 
+# namespace teaches Kustomize which fields represent a resource namespace.
 namespace:
 - kind: CustomResourceDefinition
   group: apiextensions.k8s.io
   path: spec/conversion/webhook/clientConfig/service/namespace
   create: false
-
-varReference:
-- path: metadata/annotations
diff --git a/config/default/kustomization.yaml b/config/default/kustomization.yaml
index 50a3d7a6e..7f6cd3a09 100644
--- a/config/default/kustomization.yaml
+++ b/config/default/kustomization.yaml
@@ -1,9 +1,6 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 
-configurations:
-- kustomizeconfig.yaml
-
 resources:
 - ../crd
 - ../manager
diff --git a/config/default/kustomizeconfig.yaml b/config/default/kustomizeconfig.yaml
deleted file mode 100644
index eb7da15ba..000000000
--- a/config/default/kustomizeconfig.yaml
+++ /dev/null
@@ -1,13 +0,0 @@
-# the following config is for teaching kustomize where to look at when substituting vars.
-# It requires kustomize v2.1.0 or newer to work properly.
-varReference:
-- path: spec/template/spec/containers/ports/containerPort
-  kind: Deployment
-- path: spec/template/spec/containers/volumeMounts/name
-  kind: Deployment
-- path: spec/template/spec/containers/volumeMounts/mountPath
-  kind: Deployment
-- path: spec/template/spec/volumes/secret/secretName
-  kind: Deployment
-- path: spec/template/spec/volumes/name
-  kind: Deployment
diff --git a/config/webhook/kustomizeconfig.yaml b/config/webhook/kustomizeconfig.yaml
index 25e21e3c9..0916ac341 100644
--- a/config/webhook/kustomizeconfig.yaml
+++ b/config/webhook/kustomizeconfig.yaml
@@ -1,5 +1,4 @@
-# the following config is for teaching kustomize where to look at when substituting vars.
-# It requires kustomize v2.1.0 or newer to work properly.
+# nameReference teaches Kustomize which fields represent a resource name.
 nameReference:
 - kind: Service
   version: v1
@@ -11,6 +10,7 @@ nameReference:
     group: admissionregistration.k8s.io
     path: webhooks/clientConfig/service/name
 
+# namespace teaches Kustomize which fields represent a resource namespace.
 namespace:
 - kind: MutatingWebhookConfiguration
   group: admissionregistration.k8s.io
@@ -20,6 +20,3 @@ namespace:
   group: admissionregistration.k8s.io
   path: webhooks/clientConfig/service/namespace
   create: true
-
-varReference:
-- path: metadata/annotations