I recently completed the paintjob on our SpaceWhale bobblehead. The colour variants are simply a hue shift applied to the diffuse / albedo values, and a value / colour gradient on the emmissive mask / texture. So that level of customization may be available at some point in game.
What colour scheme do you like most?
The SpaceWhale “Whale” version of the bobblehead (tophat monocle ) is also being considered as the default bobble for backers.