First of all, I am making a game (funny you say so) but this part is only the tool you use to make tilesets. The problem with this is, lets say I have a 256 tile tileset (worst case scenario), then it has to store 512 images. I dont think its worth storing the same image twice for every tile in the game. So, until I can think of something better, the only thing to do is select the transparent color and hope the user can tell whether it works or not.