Absolutely, keeping quail and chickens on a farm, you need to practice bio security. If you have walk in quail aviaries and walk in chicken yards, you will need to change your shoes between species. You would need to keep the species separated a good distance so things can not float over and never share water or feed dishes. You would need to wash your hands between the species and if warranted, you might have to change your clothes if you were really doing some cleaning in one of the areas. So yes, disease can happen if you are not careful.
As for raising them together...Chickens can still be carriers of things right out of the egg. Another problem that arises when raising them together is that they each have their feed requirements...quail as babies need about 28% protein for proper growth, where as chicken babies can get by on 18%. This also goes for adult quail and chickens as well. So if you brooding these two species together, one of them is either going to get far too much protein or far too little protein. If you brooded them along side each other, but separated as you mentioned, again, there is still possibility of disease transfer. Things float, sneezes fly and your hands will transfer disease if not washed.
As for adult quail and chickens, again, the feed requirement is so different. And you can not feed layer feed to male quail. It will destroy the kidneys. Chickens are very large and aggressive chickens will kill quail.
So the long and short of it is, quail need their own housing away from the chickens.
