How are there skeletons in the landscape?

[Cleretic]

Things we kill dissolve into aether because that’s just what happens in video games.

In-universe that doesn’t happen or else no one would be able to harvest bones/furs etc. or even eat meat.

It's actually been a staple thing even back as far as FFII: when characters die, their body fades away. And despite that, yes, there are undead enemies in FFII; it was actually the game to introduce the idea of healing magic hurting undead.

In modern games this would be a classic bit of narrative-mechanic synergy, because... well, dead bodies fade away in gameplay, why wouldn't they fade away in cutscenes? Except that didn't happen in FFII, or in fact any FF game until like FFX, dead enemies disappear in a completely different way!