There's something about a Mario with blow-up fists that just runs around being a contrary jerk to everyone while repeating the same quotes over and over... I dunno, it just makes me laugh. And I don't have a better explanation for Yoshi not being able to go into those fortress levels.
In this flashback we see Yoshi revisiting the days of Super Mario World! Fully clothed, and not carrying the titular hero around at all. What does this mean?
It means I have no idea what I'm doing. Current canon to the comic - Yoshi was always civilised, clothed and a bit stupid. He got the Pegasus Boots (Those Sonic shoes) later and they became a standard part of his wardrobe. Yoshi was involved (Barely) in the events of Super Mario World, but wasn't a part of Super Mario World 2 or Yoshi's Story.
This is all subject to change whenever I please.
I hope you got all that, there will be a test before the end of class.
Oh, and with regards to Magenta's analysis of the magic, I guess she just learned the telltale signs of magical interference while working for Bowser. Dude's got a lot of Magikoopas around, and magic is rarely a subtle thing in the world of Nintendo.