Microsoft article talks about how Azure Monitor can be used to scrape Prometheus Metrics. The scope of this question is limited to K8 cluster monitoring (not workload/apps deployed on it). Based on my understanding, even Prometheus uses agents(also called exporters) to publish the metrics exposed by K8 API server (typically /metrics endpoint) and then Prometheus scrapes metrics through these endpoints.
Azure Monitor for containers also does same thing (collecting from API server) and even more. It provides pretty exhaustive list of metrics.
My question is: Unless I'm looking at app/workload integration (or Prometheus format) am I missing anything iof I use just Azure Monitor for containers and not really scrape Prometheus metrics of my AKS cluster/nodes/pods/api server etc.?
No, is perfectly fine to collect only the cluster metrics if you need them.
In the "prometheus-data-collection-settings" just leave the monitor_kubernetes_pods to false.
Just keep in mind all this discussion makes sense only if you care about getting your metrics using the Prometheus endpoints; in general, AKS emits metrics already on its own you can check in Azure Monitor.