once you try the tool it will make sense, why I did things this way, but when you select the body handle the spheres that are part of the active sphere group highlight and the ones not selected will receed. it is also good to have the other spheres visible so you don't leave gaps between say(hip's and chest etc...). anyway once playing with it, it will feel like a fisher price ragdoll tool and the process of doing it is over so quick it's not worth all the extra work to apply such a feature.
this will be an executable not a 3drad project, so you won't have to worry about the left side if that's what you are talking about as busy.
edit: oh sorry you were talking about rads(me commenting before reading properly again my bad) object list, what I did to get around that was change the color scheme of the 3drad ui elements and chose darker colours to provide better contrast agains the lighter unselected items. you get used to it and although collapsable item groups would be cool, changeing the color scheme works well too.