I don't doubt there are lots of chemical changes when various base grains/foods are fermented. I don't have much doubt about improved digestability for the chickens either.I'm still reading. It matters what exactly you are fermenting and which fermenting process one uses, right?
"The content and quality of cereal proteins may be improved by fermentation (Wang and Fields 1978; Cahvan et al. 1988). Natural fermentation of cereals increases their relative nutritive value and available lysine (Hamad and Fields 1979) (Fig. 4). Bacterial fermentations involving proteolytic activity are expected to increase the biological availability of essential amino acids more so than yeast fermentations which mainly degrade carbohydrates (Chaven and Kadam 1989). Starch and fiber tend to decrease during fermentation of cereals (El-Tinay et al. 1979). Although it would not be expected that fermentation would alter the mineral content of the product, the hydrolysis of chelating agents such as phytic acid during fermentation, improves the bioavailability of minerals. Changes in the vitamin content of cereals with fermentation vary according to the fermentation process, and the raw material used in the fermentation. B group vitamins generally show an increase on fermentation (Chavan et al. 1989) (Fig. 5). During the fermentation of maize or kaffircorn in the preparation of kaffir beer, thiamine levels are virtually unchanged, but riboflavin and niacin contents almost double (Steinkraus 1994)."
There is something in the back of my mind I think I learnt regarding proteins that makes me doubt that the actual protein content changes; I just can't drag up the relevant science at the moment.