https://github.com/openshift/prometheus-operator/pull/86 backported a critical fix to prometheus-operator 0.40 (the version that is currently being used downstream) The problem is that 0.40.1 will never be released upstream due to a n-1 release policy (the current release is 0.42 which already includes the fix). Hence, in the interest of supporting an long term version of prometheus-operator we have to be in sync with upstream as close as possible and should use a vanilla upstream operator as much as possible.
tested with 4.6.0-0.nightly-2020-09-22-000541, prometheus-operator version is 0.42.0 now # oc -n openshift-monitoring logs $(oc -n openshift-monitoring get po | grep prometheus-operator | awk '{print $1}') -c prometheus-operator ts=2020-09-22T05:06:20.524409573Z caller=main.go:219 msg="Starting Prometheus Operator version '0.42.0'."
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 4.6 GA Images), 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-2020:4196