Everything in the entire book ties together and leads logically to the conclusion. Every. Single. Thing. Even things you thought were throwaway one-liner jokes. Even lines you'd completely forgotten.
In chapter two of the book, one of the paragraphs implied that the Electric Monk was actually built by aliens and was designed in a way that just so happened to make it look like a human. That also explains why donkeys would have to "be built" like the chapter says they are. The whole chapter takes place on an alien planet and presumably donkeys don't exist on it, hence why the aliens had to make them. It also explains the pink sand and a whole ton of other things.
The Brandenburg Concertos didn't need to be dropped into J.S.Bach's mind. The story of the Brandenburg Concertos is an odd one: they are believed to have been written as a job application (to be court composer) by J.S. Bach in the early 18th century, sent to the court of Brandenburg and pretty much ignored—shoved in a cupboard and never played, and they were pretty much totally forgotten about for 200 years. They were found in the cupboard in 1925, after J.S. Bach's fame was assured. Musical historians in the real world have no doubt that J.S. Bach wrote them.
In Season 2, the One-Eyed, One-Horned Flying Purple People Eater is a scary purple monster that attacks people. In the actual song, however, the monster is of unknown color, only eats "purple people," and is friendly to humans. The boy who created the Purple People Eater was apparently too young to understand the wordplay of the song and get the joke.
How did the Mage go from the Harmless Villain that Francis meant for him to be to the unstoppable menace we actually see in the show? Because Francis made a mistake when creating Wendimoor that he was then unable to correct - somehow, the Mage ended up with an entire army of Kellum Knights. He was supposed to have ten. No wonder all those battles he was meant to lose turned out to be easy wins for him.