PNG does not allow alpha layers, so it might be difficult to add colour schemes with just one sprite.
Distant worlds used 'pure' colours for various effects on their sprites. Pure blue, for example, (0.255.0) was used for drives. A line of pixels of this colour was used by the game as a starting point for drive effects. This might be used in SF for colouring schemes, but i really doubt that this will work properly.
Starfarer might use coordinates for this purpose (much like boarders or weapon/drives coordinates we have now). The same thing might be used for decals/icons/badges (with a single point for center of the badge image, for example, and additional info in its hull file for angles and sizes).