At the trails I ride, there is a good mix of hard tail and FS. I think the test is very controlled and well thought out. All the bikes were of the same suspension design, they did a very good job of trying minimize other effects not related to wheel size. Even though statistically they say there is no difference, the 29er coming in 12s faster on average around the loop is pretty significant.
I know when I got my 29er, I would finish my normal 10 mile loop faster than I ever did on my 26er or 69er.