I think the difference between Shrek and Knights of Guinevere is that Shrek is making fun of and criticizing the stories that disney tells, while leaving the corporation mostly unbothered while Knights of Guinevere is critizicing the corporation of disney, while still saying that their art has value for a lot of people.
Like, Shrek literally begins with him wiping his ass with a storybook page, intended to parody the beginning of a lot of early disney movies, but the story being told (Fiona's backstory) did happen in universe. Princesses, dragons, talking animals and puppets, fairies and ogres all exist within Shrek, and the story tackles how these fantastical beings would act in our real world. The story is about tropes and expectations that people have when watching classical disney movies. It's about who gets to be a hero or not inside of those stories.
And it is pretty mean, but really only towards those who have been privileged in disney stories. Princes, fairies, queens and kings, the beautiful people who are praised for being beautiful and not much else. In contrast, it treats the forgotten pieces of those stories, ugly witches, talking animal sidekicks as worthy of attention, and beautiful in their own right.
In contrast, Knights of Guinever is about what happens after the credits roll, when you leave the theater and there is a shop beside it selling mickey mouse backpacks. There are no actual princesses, or mermaids, or magical creatures in this world, only the cold hard reality of existing in late capitalism. It criticizes merchandise, worker exploitation, environmental hazards, and how a company treats their stories: squeezing out every last bit of money out of it, until it's so corrupted you feel guilty for having ever enjoyed it, despite the fact the original thing is still so full of joy and wonder.
And the interesting thing is, it inadvertly criticizes Dreamworks as well, as even though they received early sucess as "disney but with farts", from the very beggining they were copying disney in regards to merchandize, advertisement, theme parks, etc. Did you know that, upon release, it was impossible to find any dolls of Fiona as her ogre form, because her princess form tested better with little girls who wanted to play as disney princesses? In spite of their messaging that Fiona was just as beautiful and deserving of love as an ogre, when it came to making money, they followed disney's formula exactly.