While debugging other issues I was having with the ABI, I attempted to use the MCO to specify an alternate NTP server for chrony to use. Once the guests start (but before the install process completes) I ssh'ed to each agent and noticed that the /etc/chrony.conf was not the chrony.conf I specified in my custom manifests. 

    openshift-install 4.16

    Consistent

    1. Create an agent-config.yaml and install-config.yaml inside a directory (in my case `manifest-dir`)
    2. Create a custom chrony config, then use butane to convert the config to suitable 99-master-chrony.yaml and 99-worker-chrony.yaml. Inside the `manifest-dir` create a directory called `openshift` and place the resultant 99-master-chrony.yaml and 99-worker-chrony.yaml files in the `openshift` directory (I followed these instructions to create my MCO object: https://docs.openshift.com/container-platform/4.16/installing/install_config/installing-customizing.html#installation-special-config-chrony_installing-customizing and these instructions for concerning the additional configuration: https://docs.openshift.com/container-platform/4.16/installing/installing_with_agent_based_installer/installing-with-agent-based-installer.html#installing-ocp-agent-opt-manifests_installing-with-agent-based-installer)
    3. Create the agent install images with the openshift-install binary
    4. Boot the agent iso's, ssh to an agent and review the contents of /etc/chrony.conf. Note that the contents of /etc/chrony.conf are not the same as the custom configuration.
    

[core@manager0 ~]$ cat /etc/chrony.conf
# Use public servers from the pool.ntp.org project.
# Please consider joining the pool (https://www.pool.ntp.org/join.html).
pool 2.rhel.pool.ntp.org iburst
# Use NTP servers from DHCP.
sourcedir /run/chrony-dhcp
# Record the rate at which the system clock gains/losses time.
driftfile /var/lib/chrony/drift
...

    The /etc/chrony.conf contains my custom configuration settings

    This is the contents of my 99-master-chrony.yaml (the worker's was similar besides substituing master for worker):
apiVersion: machineconfiguration.openshift.io/v1
kind: MachineConfig
metadata:
  labels:
    machineconfiguration.openshift.io/role: master
  name: 99-master-chrony
spec:
  config:
    ignition:
      version: 3.4.0
    storage:
      files:
        - contents:
            compression: ""
            source: data:,server%20ntp.my.test.domain.com%20iburst%20%0Adriftfile%20%2Fvar%2Flib%2Fchrony%2Fdrift%0Amakestep%201.0%203%0Artcsync%0Alogdir%20%2Fvar%2Flog%2Fchrony%0A
          mode: 420
          overwrite: true
          path: /etc/chrony.conf