Updating the KOTS prometheus address with a Kubernetes job. You could do something similar in an init container.

set-kots-prometheus-address.yaml

apiVersion: batch/v1
kind: Job
metadata:
  name: set-prometheus-address
spec:
  template:
    spec:
      containers:
      - image: nicolaka/netshoot
        name: set-prometheus-address
        command: 
          - bash
          - "-c"
          - | 
            curl http://kotsadm:3000/api/v1/prometheus -X POST -d '{ "value": "http://prometheus-kube-prometheus-prometheus.monitoring.svc:9090" }' -H "Authorization: ${AUTH_STRING}"
        env:
        - name: AUTH_STRING
          valueFrom:
            secretKeyRef:
              name: kotsadm-authstring 
              key: kotsadm-authstring
      restartPolicy: Never