Adapting a show to screen isn’t always easy; we have to see dialogue and aren’t in the heads of the characters, and exposition needs a dedicated excitement to keep viewer interest. It is of no surprise that the show runners tweaked and modified Lev Grossman’s source material (The Magician’s novels) when creating the show. I won’t go into analyzing all of the differences and nuances that were changed, but there’s one fan accepted explanation that has always bothered me (I felt that eye-roll, just hear me out).

Source: The Magicians SYFY
The Magicians on SYFY got a great plot device in the time loop storyline to explain any differences and not have to adhere to the original in the explanation that, “this is just a seperate time loop from the books storyline and thus our characters are slightly different and their experiences are slightly different.”
This was directly referenced when the group first reaches The Neitherlands in the show and the head librarian calls Margo by her book name “Janet”, and upon being corrected comments on how Margo is just her name “this time.”
The whole concept helped a lot for pre-show books fans adapt to the changes the show made to the story, including helping me deal with my own hesitations about them, but then the show shot itself in the foot with its own explanation: they killed Jane Chatwin.
Jane Chatwin was the recurring character that guided the events of the first book, and was responsible for the time loops in both universes. The problem we run into with the, “Oh it’s an alternate timeline, so everything works and everything is canon,” is that, in BOTH timelines the time-loops are ended; Jane Chatwin dies in the show, but destroyed her time-loop device in the books.
Both the show and the books claim to be the definitive final timeline, and both can’t be right. So, which is canon? Lev has been gracious about praise for the series taking his world into directions he hadn’t thought of, but that doesn’t make it better or worse, just different. I think it comes down to the books being full canon and the show not being part of the same time loop, but making the show morr of a full blown AU akin to fan fiction [which helps explain the dramatic differences in themes].
Bold claim, but here’s my argument–The alternate timeline doesn’t work. In show canon, SYFY ran a contest called “Battle the Beast” that encouraged fans to speculate and write fan fiction for “the other 39 encounters with The Beast.”
The wording in the explanation of the official contest discredits the book as being one of the time-loops shared in the universe of the show, and it draws a line in the sand that the show is more of a complete alternate universe than simply an alternate timeline.
To the shows credit, it is an officially licensed AU supported by the original author, and without it we wouldn’t get all the fun cgi, visual representations, new storylines (the best parts of the show are when they go entirely off book), the inclusion of more lgbt and poc characters on tv, or all the nice official merch they (finally) released!
(Honestly? Waiting until the end of a second season to release official merch, after shutting down the fan-run cafe press? That’s just rude, and the only real complaint we have with the handling of the show!)
What if Jane reset the loop before she distroyed the clock in the book
It seems like you’re under the impression that the characters can’t change. However, that is not the case. We already know that Margo’s name was Janet in another timeline.