You've changed your question from how do people do it so often to how do you do it under your circumstances. It's obvious from your question that some people do often manage.
It's true that male and female ducks have different reproductive equipment than chickens. As aquatic birds they developed a way to be ale to breed in the water without the water causing a problem. The mating is kind of explosive to prevent the water from getting in. And the males equipment is fairly large. If a drake mates with a chicken hen and if he lines the equipment up properly to achieve penetration he could cause damage. "If" is always possible even if it doesn't happen that often.
We all have different circumstances, that's why what works for some people doesn't work for others. That could be facilities, flock make-up, many different things. So how do you manage with your circumstances? I'd go by what the others are saying and keep them separated. Whether separated means fences, re-homing, or eating is your choice.