Upgraded successfully from 4.2.0-0.nightly-2020-06-11-073537 to 4.3.0-0.nightly-2020-06-16-203431 with custom ContainerRuntimeConfig.

$ oc get clusterversion
NAME      VERSION                             AVAILABLE   PROGRESSING   SINCE   STATUS
version   4.2.0-0.nightly-2020-06-11-073537   True        False         162m    Cluster version is 4.2.0-0.nightly-2020-06-11-073537

$ cat ctrcfg.yaml 
apiVersion: machineconfiguration.openshift.io/v1
kind: ContainerRuntimeConfig
metadata:
  name: custom-ctrcfg
spec:
  machineConfigPoolSelector:
    matchLabels:
      custom: pids-limit
  containerRuntimeConfig:
    pidsLimit: 8192

$ oc create -f ctrcfg.yaml 
containerruntimeconfig.machineconfiguration.openshift.io/custom-ctrcfg created


$ oc adm upgrade --to-image=registry.svc.ci.openshift.org/ocp/release:4.3.0-0.nightly-2020-06-16-203431 --allow-explicit-upgrade=true --force
Updating to release image registry.svc.ci.openshift.org/ocp/release:4.3.0-0.nightly-2020-06-16-203431

$ oc get clusterversion
NAME      VERSION                             AVAILABLE   PROGRESSING   SINCE   STATUS
version   4.3.0-0.nightly-2020-06-16-203431   True        False         73s     Cluster version is 4.3.0-0.nightly-2020-06-16-203431

$ oc describe clusterversion
Name:         version
Namespace:    
Labels:       <none>
Annotations:  <none>
API Version:  config.openshift.io/v1
Kind:         ClusterVersion
Metadata:
  Creation Timestamp:  2020-06-17T13:10:29Z
  Generation:          2
  Resource Version:    62630
  Self Link:           /apis/config.openshift.io/v1/clusterversions/version
  UID:                 eabd4b39-b09b-11ea-ad72-024681d1b312
Spec:
  Channel:     stable-4.2
  Cluster ID:  f9c138f8-3986-42e4-b376-2824196a6b4b
  Desired Update:
    Force:    true
    Image:    registry.svc.ci.openshift.org/ocp/release:4.3.0-0.nightly-2020-06-16-203431
    Version:  
  Upstream:   https://api.openshift.com/api/upgrades_info/v1/graph
Status:
  Available Updates:  <nil>
  Conditions:
    Last Transition Time:  2020-06-17T13:30:05Z
    Message:               Done applying 4.3.0-0.nightly-2020-06-16-203431
    Status:                True
    Type:                  Available
    Last Transition Time:  2020-06-17T14:55:53Z
    Status:                False
    Type:                  Failing
    Last Transition Time:  2020-06-17T15:01:40Z
    Message:               Cluster version is 4.3.0-0.nightly-2020-06-16-203431
    Status:                False
    Type:                  Progressing
    Last Transition Time:  2020-06-17T13:10:42Z
    Message:               Unable to retrieve available updates: currently installed version 4.3.0-0.nightly-2020-06-16-203431 not found in the "stable-4.2" channel
    Reason:                VersionNotFound
    Status:                False
    Type:                  RetrievedUpdates
  Desired:
    Force:    true
    Image:    registry.svc.ci.openshift.org/ocp/release:4.3.0-0.nightly-2020-06-16-203431
    Version:  4.3.0-0.nightly-2020-06-16-203431
  History:
    Completion Time:    2020-06-17T15:01:40Z
    Image:              registry.svc.ci.openshift.org/ocp/release:4.3.0-0.nightly-2020-06-16-203431
    Started Time:       2020-06-17T14:18:21Z
    State:              Completed
    Verified:           false
    Version:            4.3.0-0.nightly-2020-06-16-203431
    Completion Time:    2020-06-17T13:30:05Z
    Image:              registry.svc.ci.openshift.org/ocp/release@sha256:9d91955662cb924e534ba4123cd2a6323f954c38962c6f63d7ced232173e3a0f
    Started Time:       2020-06-17T13:10:42Z
    State:              Completed
    Verified:           false
    Version:            4.2.0-0.nightly-2020-06-11-073537
  Observed Generation:  2
  Version Hash:         V7znRRDH138=
Events:                 <none>

$ oc describe containerruntimeconfig
Name:         custom-ctrcfg
Namespace:    
Labels:       <none>
Annotations:  <none>
API Version:  machineconfiguration.openshift.io/v1
Kind:         ContainerRuntimeConfig
Metadata:
  Creation Timestamp:  2020-06-17T14:10:20Z
  Finalizers:
    99-worker-485d99cf-b09c-11ea-ad72-024681d1b312-containerruntime
  Generation:        1
  Resource Version:  29241
  Self Link:         /apis/machineconfiguration.openshift.io/v1/containerruntimeconfigs/custom-ctrcfg
  UID:               478402ec-b0a4-11ea-9cb2-0229456a6bf0
Spec:
  Container Runtime Config:
    Pids Limit:  8192
  Machine Config Pool Selector:
    Match Labels
      Custom:  pids-limit
Status:
  Conditions:
    Last Transition Time:  2020-06-17T14:10:20Z
    Message:               Success
    Status:                True
    Type:                  Success
  Observed Generation:     1
Events:                    <none>

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, 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-2020:2589