I think it was Food, Inc, a documentary from a number of years ago. Joel Salatin of Polyface Farms talks about factory farming and Salatin often argues that industrial farming is not necessarily more cost-effective and that his method is both profitable and environmentally sustainable.

People want lots of things to be cheap but that doesn’t mean it’s sustainable. Here in the mid-Atlantic we’ve seen the same thing others mention: the local, non-factory farms prices haven’t changed in years but the supermarket stuff went from being cheaper to more expensive.

The theory that optimizing for the lowest price might other negative effects isn’t exactly novel: we’ve seen that in many other areas, and if you’ve ever been anywhere near a factory farm it’s enough to put you off of eating eggs.

"Domesticated chickens may become infected by wild waterfowl or by other infected poultry", and other infected poultry includes domesticated chickens. Nowhere in that web page does it say that domesticated chickens cannot spread it to other domesticated chickens. Once a domesticated chicken becomes infected (however it became infected) in a massive concentrated area, it will spread that infection to other domesticated chickens. You're conflating "spreading across chicken farms by flight" with "spreading within chicken farms by already infected chickens" and saying the first is true so therefore the second can be.