Potentially you could create a template where the color behind the folders and dock were actually X% lighter than the rest of the background and hope that after the OS adjusts they end up matching. It would take some trial and error though, and you'd have to know exactly where you were going to have folders.
yeah that seems to be the most probable solution.
what makes it even more difficult is certain shades of grey will cause the folders to go lighter while others cause them to go darker, there's a threshold there and I was hoping to find that perfect sweet spot in the middle.
oh well!
Take the color of your folder and then make that the color of your whole wallpaper .