Let me start with chickens have been doing just fine in the digestion department for thousands of years without humans fermenting their food.
Somewhere in your post you write that human and chicken digestive systems are similar; I'm just not seeing this. Even if one ignores those odd tacked on bits like the crop and the ceca glands, there is one major difference that stands out like a bag of stones...and that's because that's what it is. Granted, it's very strong bag. Give it time it will crush a whole corn and fire it out as a paste. Some pictures of what goes in at one end of the gizzard and what comes out at the other are instructive, or even a look next time one does a necropsy or butchers a bird to eat.
It makes the digestive process and quicker and more effective,
Then there is this.
It was found in studies (a few linked to in my article) that commercial feed which even in pelleted form traveled through a chickens digestive system faster than any other offered feeds. One suggested reason for this was the gizzard was doing a pass through rather than a grinding process. Now that's efficient, but it isn't very good for the chicken. Their gizzard muscles get weak, the digestive enzymes don't get enough time before the gizzard to do their chemical breakdown. It's a point I've mentioned in the past to people who have taken in Ex Battery hens, feed them commercial feed on arrival and gradually introduce whole grains, seeds etc.
I could draw a parallel between the current nutrition drive in the UK health system for humans, where it seems we are not eating nearly enough fiber in our diets because we're eating a lot of processed slop. It gives rise to numerous gut health related problems apparently.
Same for the chickens. They need strong gizzards and left to grind down dry whole grains and seeds that's what they develop.
As the commercial feed manufacturers have discovered, if you can get a bird to eat more they'll grow faster. Similar for egg production, there are ratios of nutrients that effect the number of eggs a hen will lay,
So, efficiency; is this a good thing or a bad thing for the chicken when it comes to their digestion. Fine I suppose if the bird is never going to eat anything else, but if stuff like this goes on for long enough generation to generation it seems possible that we will have breeds of chickens that can no longer digest natural food.
Also often over looked in some of the more enthusiastic advocates of fermented feed is the chemical changes from fermentation do increase some nutrients but they decrease others. How does one work out what nutrients from one particular grain or seed one wants to boost or reduce for a chicken? Seems a bit like throwing darts blindfold.
If keepers want to ferment wholefoods for the birds I think it's fine. I've done it myself and may do it again. What I would suggest is as wide a variety of components as one can manage. It's a bit of a learning process and the keepers I know who feed wholefoods, dry or fermented, find themselves adjusting the components over time; one can even make seasonal adjustments.