Yes, I've noticed that FBX will often include extra unselected and undesired elements in an export. A list based command line export could help -- I'll look into this soon. My UDK script uses back-end FBX but isn't designed for skeletal. I'll probably look into adding this functionality to that script (which is free.)
If you ever decide to go the route of shadow skeleton or have additional joint chains in the scene, I recommend adding an option (or by default) add the suffix *_ignore to the chains that should not be exported. That way you add legacy support for ActorX (Unreal Engine) to exclude them and it should be easy to filter out…
v1.05 is released and contains a few bug fixes as well as some new features. New Features in v1.05: Skeleton Library: The Rigging Toolbox now has the ability to save and load skeletons in a proprietary format independent of Maya scenes and versions. Skeleton data is saved in a skeleton config file in the current Maya…