Hope this helps some, this is what I do.. and while it works for the the extra image folders, it doesn't get rid of all the region folders that get created inside the image types you want to keep, I never figured out a way around that.
Create your platform. Edit, and change your platform's paths, set what you want to use to where you want, and for anything you DON"T want to use, change the path to something, like JUNK. This will make a catch all folder that is in the Launchbox root that any folders you don't want showing up will point to, since leaving the folder field blank just makes it recreate what's missing. Wile It's not a perfect solution, it helps keep the folder count down. Unfortunately you have to do this on every platform after it's created, then go delete the folders it made under the platform's folder.