Alright, I didn't watch the whole video, I skipped to 16:10 and let me see if I can understand this.
Mileena, Alien, Johnny Cage, Sonya, Takeda, Kano and D'vorah are characters who probably have very few losing MUs in their best variation, so that's why they're considered S tier. (Piercing, Acidic or Tarkatan not sure lol, A-list, Demolition, Ronin, Cutthroat and Swarm Queen). The fact that they're all REALLY strong characters is enough for them to be S tier in your list and the fact that they aren't is stupid, but let's just leave it at that.
Now, let's assume that Piercing Mileena is the best variation in the game, has only 1 losing MU and that is against Acidic Alien. But if Mileena switches to, let's say, Ethereal and goes even or beats Acidic, doesn't that make her even stronger?
You're talking about a character in their strongest variation that can use their other variations to back up their bad MUs, but your logic isn't making any sense here regarding some of the placements in your list.