That is part of it. Cunego's only competition in that Giro was his own teammate, Simoni. If Simoni would not have had to deal with issues about attacking his teammate, he probably would have won. That was the Giro where no one showed up or they were not in form. Petacchi won nine stages. That says a lot right there.
On top of that I think it is likely that Cunego was--to use Big Boat's terminology--super jacked. There are several riders from around that time who had amazing performances. As the anti-doping efforts hotted up, these riders lost some of what made them special. Maybe they feared what getting caught would do to their lives. Maybe they just did not like some of the more far out doping stuff like transfusions. Who knows. But riders like Cunego, Zabriskie, and others are not the same riders they used to be.
Cunego is now mainly a one day racer. Anything beyond a week or involving really serious high mountain climbing is beyond him. I think it also indicates that although the peloton may be cleaner, the top GT guys are still heavily doped.