Success over here, too. Applying the theme and then Enabling DockMod from the menu bar did the trick. So, so much better. But now I, too, am wondering if it's possible to have a completely transparent dock.
Not sure if you can get 100% as I still see the diagonal edges very faintly but you can indeed make the dock 'mostly' transparent.
Also not sure if this works on the side dock haven't bothered to test yet.
Attached is the basic settings to do so and what it looks like. (also have a black background overlaid on my wallpaper with GeekTool.