The Isometric Orientation option for tilesets only exists to help additional tools like Terrain, Wang Tiles and the Tile Collision Editor to visualize their information better on the tile. As you noticed, it does not affect the way the tiles are cut from the image.
But actually, for tiles like you have there, it would make a lot of sense to add isometric tile cutting and it’s something I’ve been wanting to add to Tiled. It makes sense for reducing texture size and can also reduce the load on fill rate (though not in Tiled itself, since it draws tiles as rectangles). Finally it can be helpful for the artist to be able to simply render tiles next to each other that should connect. It has been discussed before and there is the following related issue about this: