The only way you can keep them separated is if you have a lot of space or you keep them penned up all the time, which comes with its own set of issues.
So reality dictates the numbers. If you don't have the space, you can't have the numbers. Pens must be of adequate size when unconfined ranging isn't possible.
Ducks are not messy if you have natural water sources. We have had multiple roosters together for a very long time, and if you give them enough space and take care of them properly, you do not have as much trouble as everyone claims you do.
You obviously haven't noticed the number of posts that exist on this forum in relation to injuries and stress that occurs from keeping multiple roosters/ different avian species together. After more than 30 years of learning how to take care of a flock properly, I won't argue with what I've witnessed or experts I've learned from.
Diseases are a chance, but here we do not have any reported. Chickens also get diseases, countless deadly ones, from the dirt, worms, and native birds. Again, the only way you can stop this is if you house them like commercial poultry operations. I would rather someone free ranged multiple species than had a completely sterile environment for their chickens. Universities also promote commercial operations. But we are not talking about diseases.
Being aware of climatic and environmental conditions which determine the existence of particular diseases/ parasites is how flock health is managed. Suggesting the only alternative to free range is a "commercial operation" is quite ignorant. Adequate range space can be achieved without resorting to a "commercial operation", and no, Universities commonly address backyard flock management:
University of Kentucky: http://www2.ca.uky.edu/smallflocks/home.html
North Carolina State: http://poultry.ces.ncsu.edu/small-flock-management-resources/
UC Davis: http://animalscience.ucdavis.edu/Avian/sm_flock.htm
University of Florida: http://edis.ifas.ufl.edu/an239
etcetera, etcetera....
