I think the thing to keep in mind about Elpis and Amaurot isn't that it shows that they're worse, but that they're the same but in a much more powerful state. I mean, we're comparing them to the Scions because of similar actions, but the Scions are all basically confirmably Good People, while Elpis is instead full of people just doing their job with varying levels of morality about it. Realistically we should be comparing them more to a city full of regular people, like Sharlayan, Limsa or Ul'Dah, where they probably come out roughly equal all things considered (once you accept that Ul'Dah's main problem is that its worst people are all at the top).

However, those average people with average levels of morality who perhaps haven't figured out the customs we know are in a rather different place in Elpis, and are responsible for things with long-reaching effects. Someone who's kind of iffy about how they take care of animals in Limsa might be bad, but they won't affect much; that exact person in Elpis has effects that are felt twelve thousand years later. To a degree this is just a consequence of where the story put them, which sort of leads to them being an answer to a philosophical question; an all-knowing, seeing, and loving god can't be responsible for our world, because they wouldn't allow bad things in it, so that god must be imperfect. And in FFXIV, the answer to that is 'the people who made this world were as human as humans, which means some were kinda dumb and kinda terrible'; nobody can invent an apex predator and also be a good person, so therefore since apex predators were invented, their creators must not be good people.

Which then leads to a 'with great power comes great responsibility' situation; we hold these people to higher scrutiny, because their missteps do more damage.