I would assume, and of course this is an assumption based on basic genetics, that given the black (blue, Lavender, silver etc) and brown, (chocolate, fawn, cream etc) base and dilutions there of, that do not exist commonly in nature, where of course all of our Muscovy originated, that any bird has a good chance of being inter bred with other breeds some where along the line of the thousands of years they have lived in domestication. They don't have the tight genetic string that dogs for example do. Thus the colors are more likely created by cross breeding, then due to selection. One can argue that mutations have occurred over the very long domestic history of the Muscovy, as we know they have, however it is more likely that since they are ducks (of sorts), and since they were owned in respect by farmers that probably did not segregate flocks, some if not allot of hybridization has occurred over hundreds of years if not more. 
We do know that the Comb duck was instrumental in the modern Muscovy, which also leads to the question, why doesn't comb duck traits occasionally appear? Do some of the mutations go back to this cross?