Colors are not saved into PSD intentionally. When changing the RGB values from code they are done on the actual representation of the image loaded up on GPU, and they can somehow decrease the quality of the image a bit in some circumstances. On an exported PNG this isn’t really noticeable unless you are saving your character on a transparent background, so I wanted to maintain the original quality of each layer by not applying any coloring on top. Changing colors is easy enough in both PS and GIMP with a much wider toolset compared to a single color picker that is available in the software. As I see it generates confusion though, so I’ll add a message box saying the same in the software so it’ll be obvious in the future that this isn’t a bug.
As for panties not loading at all, can you elaborate on that, so I can investigate the issue? Just did a quick export check and all layers are exported well in all combinations (panties, underwear, pants, and tops). Thank you!