Which one of those references has test results for soil carbon in those soils fertilized with raw manure vs. liquid digester effluent?  That is what we are debating, after all.
None here or elsewhere that I am aware of (with the caveat that I'm not a soil scientist), which is part of my point. Most of the work in this area is looking at the effects on constituents such as NPK. The relationships between soil arbuscular mycorrhizal fungi, glomalin, SOM (Soil Organic Matter), soil microbial diversity and soil management (tillage practices, fertilizer application, crop residues) are very complex and dynamic. This  is a very active research area. Glomalin was only recognized in the late 90's and it appears that there is still considerable controversy on the best techniques to measure SOM. With all the negative connotations of dirt, soil is a very complex but critical environment. Thus we are again perturbing a very complex system, potentially adversely, that we don't yet understand (IMO) sufficiently. Hence the word "may" in my original comment.

Several blogs that cover topics in this area are Muck and Mystery  http://www.garyjones.org/mt/ and Transect Points http://transectpoints.blogspot.com/