You can load and save things like actions, patterns, shapes etc from ant to any folder you want to. Photoshop I believe will remember where for example you loaded or Saved your last actions from and when to go to load or save an action set will default to the folder you last loaded from or saver to. Photoshop may default to an Userid AppData folder if you never load and saved an action or other item type. However If you save into Photoshop presets sub-folder for the type item the load item name list Photoshop displays in some menu may grow larger then can be displayed in some pop-up menu. It you save into you own folder the load item name list will not grow it will have Photoshop default item only and you will need to click an additional load button which should default the folder you last loaded from.
IMO its best to save and load from you own folders for all version of photoshop. You know where your add-ons are and you will not loose them
I agree about the custom folders, and since the File Structure is already created in the Program Files path, I treat those folders as "custom"
In Photoshop, Brushes are duplicated in Brush Right Click Menu, even though brushes are only located in:
C:\Program Files\Adobe\Adobe Photoshop CS6 (64 Bit)\Presets\Brushes
Loading Brushes defaults to:
C:\Users\AppData\Roaming\Adobe\Adobe Photoshop CS6\Presets\Brushes
There is no content in this location.