Verified on 4.5.0-0.nightly-2020-09-14-124053. Created a custom Container Runtime Config with pid limit of 8192. Do not see non-existent label messages in logs or while describing node.

$ oc get clusterversion
NAME      VERSION                             AVAILABLE   PROGRESSING   SINCE   STATUS
version   4.5.0-0.nightly-2020-09-14-124053   True        False         141m    Cluster version is 4.5.0-0.nightly-2020-09-14-124053


$ oc get containerruntimeconfig custom-ctrcfg -o yaml
apiVersion: machineconfiguration.openshift.io/v1
kind: ContainerRuntimeConfig
metadata:
  creationTimestamp: "2020-09-17T09:04:12Z"
  finalizers:
  - 99-worker-dd657657-5ca7-445e-8358-661a6e9ecba1-containerruntime
  generation: 1
  managedFields:
  - apiVersion: machineconfiguration.openshift.io/v1
    fieldsType: FieldsV1
    fieldsV1:
      f:metadata:
        f:finalizers:
          .: {}
          v:"99-worker-dd657657-5ca7-445e-8358-661a6e9ecba1-containerruntime": {}
      f:spec:
        f:containerRuntimeConfig:
          f:logSizeMax: {}
          f:overlaySize: {}
      f:status:
        .: {}
        f:conditions: {}
        f:observedGeneration: {}
    manager: machine-config-controller
    operation: Update
    time: "2020-09-17T09:04:12Z"
  - apiVersion: machineconfiguration.openshift.io/v1
    fieldsType: FieldsV1
    fieldsV1:
      f:spec:
        .: {}
        f:containerRuntimeConfig:
          .: {}
          f:pidsLimit: {}
        f:machineConfigPoolSelector:
          .: {}
          f:matchLabels:
            .: {}
            f:custom: {}
    manager: oc
    operation: Update
    time: "2020-09-17T09:04:12Z"
  name: custom-ctrcfg
  resourceVersion: "40751"
  selfLink: /apis/machineconfiguration.openshift.io/v1/containerruntimeconfigs/custom-ctrcfg
  uid: dfe48eb8-14b2-4a5f-bbd0-3919294b1648
spec:
  containerRuntimeConfig:
    pidsLimit: 8192
  machineConfigPoolSelector:
    matchLabels:
      custom: pids-limit
status:
  conditions:
  - lastTransitionTime: "2020-09-17T09:04:12Z"
    message: Success
    status: "True"
    type: Success
  observedGeneration: 1

Since the problem described in this bug report should be
resolved in a recent advisory, it has been closed with a
resolution of ERRATA.

For information on the advisory (OpenShift Container Platform 4.5.11 bug fix update), and where to find the updated
files, follow the link below.

If the solution does not work for you, open a new bug report.

https://access.redhat.com/errata/RHBA-2020:3719