I could be wrong (probably am) but, as far as I can tell the toolbars aren't in a separate folder. So, I'm thinking that window in WB configuration is just accessing and showing the toolbar files within the skins' folder. You can go into the folders and open the the toolbar folder and then compare one at a time to the tool bar list to figure it out, but is it really worth the effort?
I have 14 default toolbar glyphs - not counting the default one on the left end of the list - 2 don't show any preview and 1 of the 12 others is not default icons in the preview.
For the longest time I thought it was just showing duplicates in that it was the same folder. But it's not. In order for it to really disappear without user intervention each skinner would have to include some type of script to go find and use the default instead of including it. I got enought scripts running around lost on my computer. They would have to do the same to reuse toolbar icons from one of their other skins, etc. That would only work if you had skin being accessed installed. Get way more complicated that way.
If all it's doing is showing contents to allow you to use the toolbars from one skin on another, then what's the point of deleting the skin just to make that window conform to your idea of neat and tidy? Kind of like cutting off your nose to spite your face.