It seems fair to penalize a kid for sitting out a bunch of reps, and bump a kid who did it over and over and over.
But I don't think they are trying to re-order the class, just tell you who had the strongest showing. Look at what they said about the first place kid:
"Rosemy staked his claim as arguably one of the best wide receivers in this class by dominating during one-on-ones and then taking over during 7-on-7, especially in the red zone where he caught numerous touchdown passes."
The kid was the #1 performer, but they aren't willing to say he is even "one of" the best WRs in the class. So take it all with a grain of salt!
Also, they said:
"Johnson would have been much higher on this list . . . When he was out there, though, Johnson did his thing - which means he ran really crisp, precise routes, showed off really strong hands and gave some of the best corners in this class a lot of headaches. When he was competing, Johnson was one of the best receivers in the group. . . "
Doesn't sound like much of a cause for dropping anyone, unless they eventually decide he's a headache or lacks drive or something.