These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
It gets worse in chapter 10, where her full plan is revealed - the extraction of the Elements is only the beginning. After that's finished, she plans to have every organism without the proper genes in the multiverse hunted down and exterminated.
Also, the second chapter of the fic more-or-less begins with Rainbow trapped in Twilight's lab, with a device on her head, asking to be let go, and Twilight refusing. Fast forward to Double Rainboom...
Paranoia Fuel: The Irukandi jellyfish that Fluttershy is forced to swallow afflict a pony with every unpleasant symptom under the sun, steadily causing agony so intense that some ask to be killed to end the pain. Good thing they're just in a- wait, they actually exist?!