I am posting two pics of an older tsuka that I was recently working on. These photos illustrate the use of darker paper during wrapping, which is strategically placed around the menuki to lift the ito and hide the edges of the white papter wedges. The first image is a before shot, and the second one was taken during disassembly. 

This was recently brought up during a discussion with Keith Larman, he suggested that the darker paper might have been used to help the menuki "stand out" visually apart from the samekawa as in your first photo. Kinda of like creating a "shadow" background for the light colored menuki. Keith also said that he tends to use paper that matches the color of the ito regardless for hishigami.
For me, that's harder than it sounds; matching isn't very easy. There are additional issues with ink/dye bleeding out, and staining of the same'. I like your highlighting idea a lot; I've never thought of it like that before. I used the darker paper simply to cover what otherwise would be exposed white paper wedges...
I should mention that I do use black wedges regularly around the menuki (depending on the height, color, and size of the menuki). Here are a few examples of tsuka that I have used darker wedges around the menuki:
http://www.tsukamaki.net/gallery_07.htm
http://www.tsukamaki.net/gallery_08.htm
http://www.tsukamaki.net/gallery_13.htm
http://www.tsukamaki.net/gallery_14.htm
http://www.tsukamaki.net/katana3.htm