Sorry, this behavior was intended as a tradeoff, because we are finishing version 2.4 and I didn't want to make so big changes.
Pulkomandy, the project leader, had the same critic:
After 2.4 is finalized we can start handling seriously color counts <256, which means implementing it in all file formats : BMP, PNG, GIF, those for Atari, Amstrad, C64...
I felt that an additional prompt would be very annoying every time you saved. (in addition to "file exists, overwrite", and the prompt you get when you save an image with layers/animation)
Akira: I didn't want to trust the palette because it can include more colors than the original file :
- if your setting "clear palette" is "no", colors >16 or 32 are not blackened on loading, they'll keep for example the shades from the default 256-col palette.
- in any case, grafx2 stores GUI colors in unused color slots starting from the end.