In SERVER-123131, the "isInternalQuery" field was added to $queryStats key and command issued by the server itself (i.e. mongos sending queries to mongod to run, automatic rebalancing of shards, and more) are marked as isInternalQuery: true. 

It would be helpful to extend this logic so that Cloud teams can supply an "internal query" hint for queries made that should be considered internal to the Cloud Control Plane. Some logic that functions similar to db.movies.find({ title: 'Hoppers' }, { markInternalQuery: true }) would allow us to performantly filter out queries made from the Automation Agent; today the only option is do a text filter on Application Name.