Hypothoticly, maybe...not necesarly. Just because a charcter is a good counter character for the best character in the game, it will not be enough to make him a top character if he has terrible matchups against all the others.
And so here, While Baiken has a better chance at beating the best characters in the game, Slayer has a better chance at beating more characters in the game overall. And that is what makes him get an overall higher ranking.
I feel guilty gear is more about match-ups then it is about Tiers. Tiers are good for finding overall rankings, but overall rankings dont really matter in a single fight, then only ranking that matters is the one about the 1 character you are fighting at that time. As such, sometimes a "low tier" character is good to pick, if they match up well against your oponents character.