I believe that mudokons are slightly chameleon in nature as far as skin pigmentation goes. In AE they use their skin to express emotions. The basic skin color is green but varies depending for a plethora of reasons. Here is my list of common skin colors and their meanings.
dark green-healthy
yellow green-sick or wired
pale green to brown-unhealthy
white and blue-lack of sunlight (the mineworkers)
white and purple-tomahawker or mudarcher
red-angry
blue-depressed
I'm sure there are others but that is all I can think of for now. This would also explain how Abe can sneak past guards so easily in the shadows. He uses camoflauge. Perhaps the invisibility is an enhanced form of skin color change. All the pigmentation goes away and creates the clear (invisible) mudokon.
Feel free to shoot holes in my theory.
