You could make up all kinds of scenarios. You could discount Kwan's 94 because she also competed at junior worlds that year, but then she doesn't medal until two years after winning juniors, whereas Kim won a medal the season after winning juniors. Etc etc.
But it's probably easier to just go with the actual results. It probably does penalize Kwan a bit for being talented enough to make senior worlds that young, while she was not ready to medal yet, but then others were penalized for things outside of their control , like Mao, who probably indeed would have medalled in 2006 but we have to go with facts which is that she did not. And on the flip side, one could argue that the experience of skating in senior worlds for two years without pressure does give Kwan some kind of advantage that Mao and Kim did not have because they had to wait until they were eligible.