[Com013]

I don't think the palette is important, but the color you use.
For example, white is always the coat, blue is always the belt, red the shoes, orange the gloves, and so on.
Graal is recoloring your image and replaces the colors of the image with the colors you specified in #C0 and so on.
Black stays black (although in one version it was replaced by #C5).
Any other color (like green) will be transperent.

I am not sure about this (I never tried) but this could explain your problems with transperency.

The safest way is still to use the palette of body.png and don't change it at all. Nothing can (should) go wrong then.