Would still be good to know whether sprites can be recoloured using a scheme file without having to provide hand-recoloured .pngs for every single file.
Or whether it is possible to recolour an athlete's skin using a theme file as well.
I've tested this is well: to recolour sprites from within .scheme, I'm pretty sure the source colours have to match the PNGs for any recolourings to work, which means manual recolouring if you want the lemmings' normal colourings to be different from the default.
The .theme, it seems, is able to recolour athlete's hair and clothes, but not skin. I'd agree that, if there were a way to make this possible, using .theme to create complex spriteset recolourings would certainly be easier and quicker than doing it manually.
However, there is something to be said for getting exactly the results you want by spending fifteen minutes with a decent PNG editor. For example, if I wanted Peter Parker lems with, say, brown hair, pink skin and blue clothes, I'd do this part manually (using a global flood-fill) and then use .scheme to recolour the athlete hair, skin and clothes to red, blue and red respectively for the Spider-Man costume. Since you can also specify shade recolourings from within .scheme, this is a much more versatile and targeted way to get the desired results.