I don't think this is a major story. Phelps is just saying what the majority of intelligent fans of racing (both swimming and running) are thinking when he was asked by a reporter on his thoughts about clean athletes going into the olympics.
In the past, athletes have doped to get an edge on competition at the olympics. This is not new. The Russians doped for Sochi. They probably doped for the most-recent World Cup (their group of relatively-average players were outrunning just about every team). Michael Phelps has observed the testing procedures himself and understands how athletes could circumvent the testing protocols during their training to illegally dope.
Then, with the pandemic, the opportunity to get away with doping has increased. Thus, it is reasonable to conclude that someone out there is likely doping to get an edge. Someone else is likely doping because they feel like everyone else is doing it during the pandemic.
So, when Michael Phelps is asked the question, "on a scale of 1 to 10, how clean will the Tokyo olympics be?" he responds with an answer that's effectively, 'eh, probably somewhere in the middle.'