No one? I can't image that not even the guys at Adobe know this?
If you only use the low overhead settings (Basic Telemetry, ActionScript Sampler, and CPU Usage), then the overhead of running Scout should be negligible. I'm assuming you don't have Stage3D Recording turned on - if you do, you should turn it off to measure performance.
After doing this, if Scout is showing most of the time spent in ActionScript or Rendering, then you can be certain that it's your content that's slow. Any overhead that's due to profiling would appear as part of the "Other" category.
The CPU usage reported by Scout is for Flash Player as a whole - if you're running your app in the browser, make sure there isn't other Flash content running, as this will contribute to the CPU usage. If you're seeing high CPU usage and most of the time is spent in ActionScript, you can use the ActionScript panel to see which functions are the most expensive. There's a lot of good advice on the Starling forums about how to optimise your content, and avoid common pitfalls.
Also, please make sure that you have hardware acceleration enabled - if Flash has to use software rendering, then the performance will be terrible. You can check in the Session Info panel in Scout - if it's using sofware rendering, then you'll see something along the lines of "Software Hw_disabled" in the 3D Driver Info field.
Thank you very much for your detailed answer Michael!
That was very helpful indeed.
BTW: I'm running the app on an iPad with the latest version of AIR.