Actually it is possible to alter the colors in a theme. Under the Advanced Settings of WB you can select "Force colouring support on all skins." This will allow you to adjust highlight colors and the like. You can also change the font size shape and color under the same Advanced Settings down on the lower left. As for window backgrounds you can somewhat do what you want but I don't think you will be happy with the results. Basically what you have to do is select the grey that you want and then exclude all of the apps that you want to have a white background for and they will not be skinned.

Another option to WB is StyleXP.