There are a lot of references to the book series in this episode, like Luke owning a book shop and Magnus's cats Church and Chairman Meow in the alternate reality. All of these exist in the books (though Church lived at the institute and not with Magnus in the books)
The portal to the alternate universe looks exactly like the portal from the movie adaptation of the books.
After meeting Magnus for the first time in the alternate reality Alec comments " Playing hard to get. I like a challenge." This is the exact same thing the real Magnus says of the real Alec in the episode 'Moo Shu to Go'.
The title of the episode is quite similar to the title of Part Two of City of Heavenly Fire, That World Inverted.