It doesn't increase the total proteins but increases the total nutrients absorbed or utilized by the digestive system. From what I can understand from all the material I've read, the carbohydrates in the grains are changed into a more useable form, as are the minerals as the phytates are removed by the fermentation process. I can only go by what I've read on the studies done and I'm no scientist, by any means, so I'm not really into the fine details. Found a few articles that explain the benefits of fermentation on the grains when it comes to monogastric digestive systems like ours..and chickens.
More about the role of phytases in increasing the nutrient value of grain feeds for nonruminants...
From what I understand, the enzymes that are increased in the small intestine by the ingestion of the LABs and prebiotics of acetobacter bacilli, have the ability to actually produce proteins that are absorbed and utilized as nutrition by the host animal on a cellular level. Now..this is where I get lost and stay lost and will willingly never try to find the rest of the reasoning behind all the microbiology behind it all.
Here's a link to the information on conjugated proteins..they are about half way down the page...
http://en.wikibooks.org/wiki/Principles_of_Biochemistry/Amino_acids_and_proteins
Suffice it to say that it appears that total nutrition absorption is changed by the simple act of fermentation and it's not just the protein, but all the minerals and vitamins as well from what I can gather from all the scientific gobbledy gook. I'm not one to look beyond a certain point on the why of things when the results are easily visible, so I'm not one to explain it all nor do I want to really know but maybe someone out there with more interest in the microbiology side of it all can help you with this.