Your screen shot shows several actual windows open, so they should be in that list. I think the ones that you have marked as "not visible" can be eliminated from the list by simply clicking them and then clicking the red close button or using command-W. I think you will see the list shorten each time you go through the 'window closing' procedure. I think they will remain closed until WC is restarted.
I was not aware of these opened but invisible windows and have no idea why they should be around, but there may be some reason the Dev is handling them in this manner. Just another task to remember when WC is started, at least if you are running short of RAM or they are causing memory leaks.