When the PTP operator is installed, it brings its own alerting rule to detect clock drift which is more reliable than the out-of-the-box NodeClockNotSynchronising and NodeClockSkewDetected alerts:

https://github.com/openshift/ptp-operator/blob/4845b7ce41f44e8e62c1a66f6a41afd400b0e466/bindata/linuxptp/ptp-daemon.yaml#L222-L255

The NodeClockNotSynchronising PromQL expression should be adjusted to "mute" itself when the PTP operator is installed.

expr: |
(
        min_over_time(node_timex_sync_status{job="node-exporter"}[5m]) == 0
        and
        node_timex_maxerror_seconds{job="node-exporter"} >= 16
)
 # addition to the upstream expression
and on() absent(up\{job="ptp-monitor-service"})