Man, 'unique' world-building is such a tricky qualifier with isekai, since so much of the genre leans on RPG staples. I got kind of bored with the standard fantasy-Europe-with-status-screens thing years ago. The ones that stick with me completely reimagine the logic of the world itself, not just the wallpaper.
Take 'Ascendance of a Bookworm'. The protagonist gets reincarnated into a medieval-ish world, but the core tension isn't about fighting a demon lord—it's about the brutal, feudal economics of paper and printing. Her knowledge of modern book production becomes her magic system. The world-building is in the bureaucratic hierarchy of the guilds, the class-based literacy, and the sheer logistical nightmare of making a simple picture book. It feels lived-in and logical, where societal advancement is the true quest.
Another is 'So I'm a Spider, So What?'. The world is a post-apocalyptic magic-scape built on the ruins of a high-tech civilization, and the System is a literal, malevolent dungeon master managing the survivors. The 'unique' part isn't just that the MC is a spider; it's the dual timeline narrative that slowly peels back the layers of why this world is so messed up. You start in a dank dungeon and end up unraveling a cosmic-scale tragedy. The rules of skills and evolution are harsh, consistent, and deeply tied to the world's broken history.
Those two nail it for me because the world isn't just a backdrop; it's the antagonist, the puzzle, and the prize all in one. You don't just explore a map, you dissect a society.