That's because integration allows them to do more :) I'm in the process of writing a game in bevy (rust game engine without editor). And most of the time so far I've spent integrating Tiled with it :)
Might as well compare Logic Pro X with Visual Studio Code. Which one is better for editing pictures?
Call me when the tile editor starts having aspirations of being an IDE.
It's not for 3d, but for 2d it allows placement of non-grid-aligned objects, has custom properties, relations between objects, object grouping, layers, types, templates and classes.
So yeah, you can use it as an editor for 2d game if you integrate it with your game. I've used unity before and I prefer tiled+bevy combo for writing 2d games even if it's more work upfront.
My point is only that MORE can be done, regardless of integration or not. What really matters is the data model and (as demonstrated by Unity) extensibility.