Resolution -- I've read your posts on this topic many times. Unfortunately, every time you use much the same support for your position and every time it falls apart in the same way. And yes you're reading this all right, it's not condescending or patronizing just matter of fact.
Hilly jungles, fallen logs and rocky terrain are all still on the ground. And where they cover the soil they are the ground.
You're also mistaken on the lives of ground birds. Ground birds in locales with a lot of rocky terrain, hills and fallen logs available utilize them -- no doubt about that. Here, wild turkeys can be found spending most of their days in flat, open fields. Quail and pheasants likewise. Yes, when "ground" birds move from one elevated place to another they will use trees, branches, logs, rocks and what have you to take the easiest route. That is not evidence that being on the ground is detrimental to their health and well being. It's a survival mechanism, he who exerts the least energy to get done what he needs to get done has the most energy to spare when he needs it. He who uses the easiest route and eats the easiest to find food lives the longest.
Large objects like those you have cited catch and hold droppings in much the same way the ground does. It sticks to rocks and fallen logs and large branches and hills just as it would a flat, mowed lawn in a suburb. Spending time on elevated features of the terrain does not eliminate or even necessarily reduce the birds' exposure to their own feces -- the ample spaces they have to roam does that.
Contact with pathogens found in manure, dander and feathers can boost the immune system. Studies have shown children reared in the homes of those who disinfect obsessively are more likely to contract illness once they enter the "real" world. In a healthy chicken reasonable contact with pathogens should be viewed positively. It allows the chicken to slowly build immunity to pathogens common to their environment.
If a farmer or backyard keeper's coop is "filthy" that's on them. Obviously "filthy" conditions will be more likely to lead to disease. That's not rocket science, but it's also not support in and of itself that a cote is a superior method of rearing chickens. It's just support that non-filthy conditions are superior for rearing chickens. But I don't think we're breaking any revolutionary thought barriers there, now are we.
As for the "swine are obliged to adapt" comment, it goes right back to the same thing: space. Given adequate space hogs are incredibly clean animals. Given space chickens (and ducks and geese and turkeys and, and, and...) can be incredibly clean animals. The elevation of that space relative to the rest of their surroundings is of no consequence. There is no problem you present as evidence in support of building a "cote" vs a "coop" that cannot be solved with more space. Plain and simple.