@danna It's probably your logic that's misaligned. Which I completely understand.
You expected the System Prefs Component path to store all created components to that location.
Whereas components live within models until you tell it to be accessible globally by saving in a defined library.
Components are containers. When you have many within a model they don't carry the same amount of overhead as groups or raw geometry.
When you make a component within a file and then use the Save As to store it all you essentially are doing is creating a SKP file that only contains the objects within the component.
To double back on why Susan is in your 'In Model' library. Every component created will be in the In Model component library unless you purge it. So if Susan was originally in the file but deleted from the model space she still remains.