What do you mean by custom skins? Most planet art is defined by certain dds images, then colors applied over the top if required.

Clouds, alraeady colored, you can recolor existing dds files to change the colors:
        <AtmosphereTextureFile>Planet_Atmosphere_Clouds_Generic_Yellow_L.dds</AtmosphereTextureFile>

The Ground cover, what tiles you can build on (Overidden by  <CustomContinent>Earth0</CustomContinent>) :
        <BaseLayerTextureFile>Planet_Base_Rock_Generic_02_Merged.dds</BaseLayerTextureFile>

The initial Colors Water(I think)
        <BaseLayerGradientFile>Planet_Base_Brown_Gradient_01.png</BaseLayerGradientFile>

The initial Colors Land (I think)
        <AltLatGradientTextureFile>Planet_Generic_Continent_Gradient_Yellow_01.png</AltLatGradientTextureFile>

Type of Polar caps, Lava or Ice.
        <PolarCapTextureFile>Planet_Cap_Generic_Lava_01.dds</PolarCapTextureFile>

You can then tweak colors by changing:-

    <BaseLayerDiffuseColor>
      <Red>255</Red>
      <Green>255</Green>
      <Blue>102</Blue>
      <Alpha>255</Alpha>
    </BaseLayerDiffuseColor>

    <EmissiveColor>
      <Red>255</Red>
      <Green>255</Green>
      <Blue>153</Blue>
      <Alpha>255</Alpha>
    </EmissiveColor>

    <PolarCapTintColor>
      <Red>255</Red>
      <Green>204</Green>
      <Blue>204</Blue>
      <Alpha>255</Alpha>
    </PolarCapTintColor>

    <AtmosphereColor>
      <Red>255</Red>
      <Green>255</Green>
      <Blue>102</Blue>
      <Alpha>255</Alpha>
    </AtmosphereColor>

    <CustomContinent>Earth0</CustomContinent>

Will overide the settings. And apply a custom look, like the current Home system planets. Theres a command like the cheat command you have to use to get the game to load custom continents, but I forgot what it is.

I thought this had more to do with where the actual hexes appear on the colony screen. Does it also relate to the configuration of continents on the planet? How would that jibe with the bumpmap/ gradient system?

Yep your right. It still uses the bumpmaps to set the colors of the continents but settign a custom continent will make sure the ground cover looks how you want it:-

  <ContinentDef>
    <InternalName>Earth0</InternalName>
    <ExcludeFromRandomGen>1</ExcludeFromRandomGen>
    <EstimatedClass>12</EstimatedClass>
    <TileCount>8</TileCount>
    <TextureTile>Planet_Continent_Earth_Merged.dds</TextureTile>
  </ContinentDef>

The Land, Continents ect.

Thats what you need the command for. To tell the game to reload assests or some such.