Local jurisdictions with "muscovy problems" brought their concerns to the FWS, thus when regulations were considered and comments requested, those interests knew to make their opinions known. Because FWS does not typically deal with "domestic" animals, they really didn't know about "our side" of things. (My understanding is that true wild, native muscovies are very different from the ones that we are used to seeing).
I know this is true from personal experience. My old friend who works for FWS is a biologist in the Migratory Birds division. I always joke that she's a Doctor of Ducks because of her PhD in wildlife management, specializing in waterfowl. Last fall I asked for her help understanding the behavior of my psycho drake and for sexing young uns. Because she deals with wild ducks, she was only able to help me on the issues of biology and not flock management. Indeed she asked why I even had pet ducks. Shes been on plenty of farms, but I guess not ones that had ducks as pets or for meat and eggs. So while possession and use of muscovies seems obvious to us, its not obvious to everyone. You dont know what you dont know. The fact that FWS has been responsive to us tells me that they werent intentionally excluding us.
My friend and Dr. Allen told me that issues with mallards are a far bigger problem for FWS than muscovies. Hybridization of the wild populations are a problem from a biological standpoint, yet different kinds of mallards are regularly released where they shouldnt be. Thats where FWS is in an uphill battle with powerful political interests; people who would spend a lot of money to have a variety of birds to hunt in a designated area, but nobody told the birds that if they dont get shot they need to stay in the designated area and only breed with their own kind. So all things considered, the muscovy issue is relatively simple and it sounds like there is a solution to more or less satisfy everyone. We can have our ducks, and local jurisdictions can decide for themselves how to handle problem ducks. For those who dont want to see the friendly ducks in the local parks eliminated or killed, they can work with said jurisdictions to see about adoption programs or oiling/shaking eggs to minimize the number of future generations, and other humane options.