I can't fault the methods used in the study. It was well thought out and sounds well executed. I do wish they would have used something like what you have (new adi). My 0000 was the only new adi guitar I have ever bought and it was the one that led me to believe the tonerite was a great benefit. All other guitars of mine were already well played before seeing the tonerite. Another nice contrast would be to have a "C" instrument for each pair that was played a goofy amount of time each day.
So a tonerite may be snake oil, but it's snake oil that seemed to work for me. In the end, if all it did was make me think my guitar sounded better... well, if I enjoyed it more as a result, then I guess the science behind it is almost secondary.
It almost reminds me of the double blind study they did with old Stradavarius and new (well made) instruments. The "expert" players couldn't tell the difference (in fact preferred the new ones). In the end, I bet they still prefer to play the old strads. What do these studies really tell us? I think it tells us that tone and how we players perceive it is not pure science.