I haven't tested Tiled to Unity in isometric mode. It may work out of the box, but there might be caveats or problems, I simply don't know. I would do some tests first using the example demo assets to make sure it behaves like you want it to.
If there is a problem let me know and I can look into it. If that problem turns out to be out of scope to fix, you can always just make the map in a grid form in Tiled, and simply display the geometry in Unity as isometric.