Hey I have a dog door and my drake has used it! Once one of our chickens came through it and jumped up on my husbands recliner while he was napping, that got him up .Well, clearly they need a "ducky door" to let themselves in! You could set up a pen for them just inside the door so that they are contained This is a long-used method for puppies... it works brilliantly for them, so it should work for ducks too right?
Story. Of. My. Life.