From the article:
"It's also important to note that since the modularization of X.Org, the X server isn't the only key piece of the windowing system. Of critical importance to X.Org is also the input and video drivers, X libraries, utilities, and Mesa. None of the work from any of these developers should be discounted and they all play an important role. For this article though, we only analyzed the server git tree."

Can this explain the low percentage?