I think you can set such colors in the engine, but in the finished build of the game, just a certain default color will be set. So if I understood correctly, if you choose two colors in the engine, and make the background transparent, you will most likely get 3 colors in the finished build. But as for the graphics, yes, you can create a sprite with a transparent background and export it to the engine. In general, people will evaluate your game based on the build. I hope I have not confused you ... (The question does not specify whether you are going to select these settings in the graphics editor, in the engine or in the finished build)