Why is framing the antagonists in this way necessary?
What themes or aspects of the story does this explore, that is integral to the core theme of exploring the beauty of the fleeting nature of life?

I went into this a bit elsewhere in the thread, but I think the point is that this is a setting where the innate human desire to empathize, to form bonds with others, can be a weakness. I don't think it's trying to make a philosophical point about that though, it's not saying that we should all be cold hardened killers who don't trust. It's just exploring what that would be like, the challenge and the conflict which emerge from humanity being part of a food chain which contains creatures that hunt us using our empathy as a weakness. The same way any of the antagonists challenge the protagonists. It's an interesting issue for the characters to have to overcome.

What does the story gain from including a scene where our heroic protagonist implores her party to... kill a little girl demon? And then why does the story go out of its way to justify the protagonist's point of view as ultimately the only correct one?

I think it's there just to enhance the immersion in the challenge the characters are facing. When you or I look at that particular monster, we feel the same empathy all of the ignorant people in the story feel. You and I would definitely be killed, successfully hunted, by these demons if we existed in that world. That's why they're a dangerous challenge for the protagonists to face, that's why they're scary and believable as a problem. The world in which the story takes place is exceedingly dangerous and, even though the protagonists are practically gods, there are plenty of things which could conceivably kill them, and you and I can fully understand exactly why it would work because it would work on us. Is there no value in crafting a believably dangerous monster?

In all your other examples, the monsters are unthinking magical beasts,

As far as we're told in the story, there is no difference between the chest mimics, and the random wolves, and the dragons, and the demons. They are all equally thinking or unthinking as you prefer to interpret their behavior. They are all merciless hunters who will kill you if you don't kill them first. The difference is in their appearance and in their strategy, not in their internal experience.

If they're just monsters, why does the author have to go out of their way to present them as civilized sentient beings? Can't they just be monsters?

I would argue the author goes extremely far out of their way to prove them not to be civilized beings. They are just monsters. They just want to eat you. They literally do not know the meanings of the words they say, or have any concept of the empathy which those words exploit. They are no more civilized or more sentient than the mimics or the ghost-mimics or the wolves or the giant plant. They just evolved into the niche of looking like they are, because that makes people easier to hunt.

Comrade, do you not see the similarities with what you wrote here to what Israeli's say about Palestinians?

We've all heard fascists compare various groups of people to animals. Is it therefore unacceptable to compare horses to donkeys? If I say horses are very much like donkeys, it's equivalent to fascists saying certain groups of humans are like donkeys? I just don't see it. Fascists say all kinds of shit that isn't true. That doesn't make it untrue when you say things that sound superficially similar but are fundamentally different because they regard completely different subjects. I don't see how this logic can't be used to negate all comparisons between any two things anywhere. The US can't be like the Nazis, because that sounds awfully similar to how fascists say the USSR was like the Nazis. Is that not logically the same argument you're making here? If not, what is the difference? Israelis can say shit about Palestinians that isn't true and that same thing could be true if they were saying it of a different subject. If an Israeli said Palestinians are purple or green fruits often used to make wine, it wouldn't suddenly be wrong to say that grapes are purple or green fruits often used to make wine. They're different things. Palestinians aren't demons, they aren't a magical fantasy race that evolved to eat humans. Demons in Frieren are a magical fantasy race that evolved to eat humans. They're not Palestinians. Where is the connection?