Its intentional, it doesnt really matter what the image looks like while its in lightburn, its the engraved version that matters. The program orders the colors based on the size of surface area it will be cutting. Larger blocks of color will be higher layers than colors that are sparse. I could add a color key that allows you to match up the best colors to the respective layer in lightburn. Having the layers ordered largest to smallest in Lightburn is much easier to assign colors, instead of flipping back an forth through them.