"Then we could have another option to make sure that the same color is never used twice, assuming the palette has at least as many colors as the original image."
This is what the "no color re-use" checkbox does.I have been thinking about treating different brightness levels (shadows, specular highlights) as being the same color, and mapping them to brightness levels of another color (just like in the procedural tileset generator palettes). The problem I encountered was how to objectively determine what colors are part of the same material in the original image. Do you treat neighboring pixels as being the same material?
This tool was created a few years ago before I discovered L.A.B and made the procedural tileset generator. I may take another look at this issue to improve the tool.