do we have any possibility to gather just the "high-level webapp pmi metrics (as xy.war [green on printscreen]) and ignore the low-level metrics (as servlets [orange on printscreen])"?
you can only enable/disable a module in the IntroscopeAgent.profile. The WAS Admin Console provides more granular control over which PMI metrics are reported for all consumers including Introscope: Enable PMI Module Through WebSphere Application Server Administration Console
unfortunatelly, if we enable any PMI metric in WAS (i.e. ConcurrentRequests for webapp pmi module as it is described in the link you attached), then APM automatically displays this metric (ConcurrentRequests) not just for the main webapp module (*.war), but each submodule (servlets) under the main webapp module. and in our case it means +3000 metrics/application server so around 300 000 useless metrics in APM because the technicians need/follow just the main webapp metrics during app performance tests/investigation.
We don’t have a direct mechanism at APP level or PMI Module level. You can raised this limitaiton as an Enhancement or Idea.
The only avaialble workaround would be to use METRIC SHUTOFF feature from UI applicable to all metrics