No, the guy had Traxxion set the suspension up. Nothing other than dialing it in though. He was at the races one weekend camping out. Ended up talking to Max for a while and Max offered to go over the front and rear with him and dial it in for aggressive track day riding... Traxxion didn't do any internal work though.
Raising the forks in the triples isn't just to alter ride height. It's all part of setting up the chassis.
However, the shock is ride height adjustable. The previous owner did lower the rear down a little bit from stock, but not much. I'm sure he dropped the front a line or so to compensate. However, the rear ride height on my Tuono is stock. Look at the forks on it. They're raised in the triples because that's where the bike is most happy.
The Mille's Ohlins and my Tuono's Showas both have lines on the top of the fork tube to make adjusting the height over the upper triple super easy.