Hiya,
Do you reuse these tilemapdata objects at all? If you're sharing sprite collections in these levels, you can safely share these assets - they're meant to be 1:1 with the sprite collection, but not necessarily unique for all tilemaps. This would be the recommended solution.
If not, and you don't use prefabs at all, the easiest and quickest thing to do would be to remove the [SerializeField] from tileInfo in tk2dTileMapData to stop it from serlializing to disk. The way the UI works, it won't cope with a sparse list - so stopping it saving would be your best bet here.