You stated "...so 95% of the time a Yoshi of equal level will beat a...". Which leaves Ganondorf with "5%". Five percent of the time that Ganondorf has a chance of being the one to come out on top.
In Monster Hunter, odds of carving a Plate are 5%. Which means 5 percent of the time of all the possible outcomes, the Plate is going to come out on top. I don't know how you 'figger, but they both mean the same thing to me. A percent is a percent is a fraction whatever form it comes in.
But there's more to the ratio than just random percents. I believe the better way to look it is as how many advantages one character has over the other.
-What's a distorted hitbox? lol A disjointed hitbox is a hitbox that will damage the enemy player while the attacking player is out of reach of recieving damage themselves. Like Dedede's hammer, Ike's sword, Marth's sword... I can't think of any moves offhand Ganondorf has that are disjointed. If anything, it would be his Dtilt because the hitbox extends a couple inches from his toes... which isn't really enough to be called disjointed IMO. And his leg can still be attacked.
Now I didn't say Yoshi had an infinite on Ganon... if there is a wall, then yes. Yoshi's chaingrab is the grab release, causing Ganon to jump high in the air and upon landing, Yoshi grabs again. This is done untill there is no more ground for the Yoshi to grab on, and he just drops off the ledge to a Fair spike.
If you believe Ganon has a better chance, that's fine by me. I'm just giving out my opinion here, which isn't always the best. That's why I don't post in matchup threads.