A 4/6 matchup is not that cut and dry. Take the Ganondorf vs. Mr. G&W matchup. If you look at the Ganondorf summary in the G&W matchup thread, all the G&W has to do is to not make mistakes against Ganondorf as he can capatilize on those mistakes easier than most mid/low tiers due to his range and G&W dies from 4 strong hits from the King. On the other hand, if the G&W does not give Ganondorf those opprotunities, then Ganondorf can't do ANYTHING to him and the match is an surfire victory.
What is to say that MK's 4/6 matchups are not like that. Simply put, MK has much less things that are exploitable by the other characters than G&W does. A 4/6 matchup with DDD, Snake, G&W, Falco, Diddy, Wario, and even Marth is different than a 4/6 matchup with MK as a lot of characters can exploit something those 7 top tiers have.
Here is an example, Kirby vs. MK and Kirby vs. Ice Climbers. Both are 4/6 matchups, but Kirby can at least separate the Ice Climbers and capatilize on the opprotunity to destroy Nana (though he is not as adept at that as say MK or Jigglypuff) if he lands a hit on them. What can Kirby do against MK that other characters can't though? Maybe he doesn't get overwhelmed by MK that easy, dodges his edgeguarding, and kills him earlier than someone like Peach. But Kirby can't exploit MK that easily while MK can do that to Kirby much more easily. Both MK and the Ice Climbers brickwall Kirby to an almost equal extent. But the Ice Climbers, unlike MK, have something Kirby can take advantage of somewhat easily.
tl;dr, a 4/6 matchup ratio is not to be taken very seriously as it is a very gross simplification of a dynamic between two characters.
(btw, playing Devil's Advacate here)