This has been explained many times. I will explain it again.
Secondaries do not come into play when talking about a tier list. If we are comparing DK vs Dedede, and assume that DK uses a secondary in trouble, say MK, and that Dedede therefore goes to MK as well, we get a 50:50 outcome. Is this really the truth? Is their matchup 50:50? No. Not even close. You can clearly see that DK loses lol.
Secondaries don't come into play because you can just assume for both sides either a matchup that is really close to 50:50 or a matchup ditto. These would not accurately describe/illustrate a character's potential when compared to others, because you aren't even comparing them in the first place if you just start throwing secondaries into the equation.
As for MK being the best secondary...
MK is the SAFEST overall secondary AND character to use. He's the best character in the game, this should be obvious.
It is TRUE that MK will not guarantee you the STRONGEST ADVANTAGE POSSIBLE when it comes to Specific character matchups where you employ him as a secondary. If you are playing against a Donkey Kong and want the strongest possible advantage, it is obvious that the absolute strongest choice to pick is King Dedede. This is the case for a fair number of matchups where MK may not necessarily be the character's worst matchup.
HOWEVER, if you want to play theoretical Hop Scotch, when considering what Secondary character you should use, you also have to factor in the OTHER person choosing a secondary as well.
For example, say you are playing a DK main. You are a Falco main. First round. DK player doesn't like the matchup, calls for a double blind (doesn't matter who calls for a double blind, just illustrating a scenario). Assuming you stay Falco, his strongest choice might be IC's/Marth/some character with the advantage over Falco. Say you know this and you are anticipating his switch to Marth and so you switch to MK.
Marth/IC's/etc was his strongest secondary choice, PROVIDED AND ASSUMING you stayed as Falco. If you are allowed to switch characters, then you have to factor in the opponent's possible choices and counter choices. In THAT situation where both sides are allowed to pick a character, MK is the best overall choice.
Say it is your CP however. You pick FD. Your opponent goes Falco. In this instance, it's clear that the strongest choice would be IC's/someone else that beats him on FD. The problem with this is that these "stronger" Counterpick choices/Secondary choices are not as applicable as an overall spread like MK. Going IC's on FD against Falco is fine, but what if you are up against someone on a stage that IC's struggle on? Who are you going to rely on?
Sure, you could try to pick up a plethora of characters to cover your back at all times, and even THEN it might not be enough to guarantee your safety.
Look at the perspective of the person who is getting CP'd. He has to pick first. His best option, in this spot, is to pick the character that is "safest"/has fewer bad matchups or less severe matchups than the rest of the characters. If you only have 1 55:45 matchup against you, the only way you will be at a disadvantage is if your opponent plays as that exact character. If you have 3 55:45 matchups against you, AND a 6/4 matchup against you, you not only have more characters to worry about, but you also have to worry about a stronger disadvantage being presented to you.
Basically, MK is the best secondary/character to use if you yourself are being CP'd, and he is the best secondary to use if both parties are allowed to choose their character at the same time (first round, DB or not). MK for specific matchups might not be the STRONGEST choice to make, but for the most choice he is the SMARTEST/SAFEST choice to make.