Importing isometric tiles hasn't been tested at all. I believe Tiled stores the tiles in a different way completely, making it impractical to import. I will need to check this to make sure. IIRC, the TileD tilemap is stored as indices going up in a 45deg angle.
If you have any issues importing (eg errors), try saving the TileD file as compressed.
If you want to extend the importer, it should be straightforward, its in tk2dTileMapImporter.cs, and the function you want is PopulateTilemap.