TileFlags are used to mark tiles as flipped, rotated, etc. Its defined at the top of tk2dTileMap.cs (looks like its accidentally excluded from the documentation, I'll add it in the next update). This is merged into the tileId, so isn't actually a good idea to add your own stuff into it. The easiest option is to maintain your own (2d, or flattened 1D) array the size of the tile map and then storing whatever flags in there.