It was like a totally random fanfic... but canon... some of it sorta worked... some of it was totally absurd... but it's all official canon now because nothing at the end retconned it by making it all a dream or the CMCs attempt at creative writing...
All I can say is, no true professional writer would have done this to their own material. Indeed, most writers AVOID fanon at all costs... for this very reason.
It ends up being too confusing and utterly alienates many fans of the proper canon who hate certain fanon ideas. It feels as if the writers have cherry-picked some people's ideas and slapped everyone in the face with them while ignoring everyone else's opinions.
It's a BAD IDEA. That's all there is to it. I actually chuckled at the secret agent Sweetie Drops part... which I assumed must have been an early hint that this was all going to be retconned somehow since it just made no sense outside of a fanfic about her and Lyra... and then it was suddenly canon, nothing was undone... and I got this horrible sinking sensation in my gut.
This is one of the ways series are destroyed, people. Always remember what happened with "Star Trek: Nemesis". This may very well be the Pony "Nemesis".