>>42517589
>And nobody has the foggiest idea why it was so obligatory.
I don't know why this is a mystery. For one, it's just wrong, there's tons of stories that don't respect canon much at all, from DoWaS that completely redefines how the EoH work to StN which rebuilds Ponyville into the author's twisted vision.

In general, those kinds of references are in there because they're fandom touchstones. "You remember that episode you liked? I liked it too, let's like it some more"
Furthemore, while it doesn't apply to this fic, they are also important to establish the setting when dealing with S3. Not just Twilycorn, S3 is quite densely packed with lore- and setting-impacting episodes. It's a good idea to anchor the fic to an episode like ACW to establish what the setting is like, one obvious example is that Discord can never be expected to save FS here.

>Seeing a slightly more sinister side of Celestia and Luna is quite satisfying, especially given all the full-throated service the fandom usually lavishes them with
Rariflag did mention this, but I'll repeat that it's actually just not true. I'll go further and say that it's the default state of fanfics to give both princesses a checkered past building Equestria's utopia, and it would actually be rather nice to have them unambiguously the good mares. I'm not expecting it, the fic seems to be laying an untimely death of their third sister at their hooves. But it would be nice.