All of human nutrition is extremely complex for both very sound scientific reasons and sometimes political or religious reasons. We understand rat nutrition pretty well compared to some aspects of human nutrition because studies can do things with rats that should never even be contemplated for humans. So a lot of studies are like the ones you cited, more like clinical investigations. There are some population studies, like the ongoing Framingham study.
So what you're seeing is interesting but not surprising. There is sort of a dichotomy in the current nutrition world view. This book:
Gary Taubes 2008 'Good Calories Bad Calories and the Controversial Science of Diet and Health' explains it and how it got the way it is.
Taubes is a science reporter, but this does cite quotations from interviews with scientists, peer reviewed papers, so in that sense it is reasonable. But you can see from this book that how we view Nutrition Science and what makes us fat are both undergoing a major reconsideration. Exactly how science works.
The dichotomous view is centered around fat and calories in the diet. As a simplification you can view it as:
1. A Low fat, high carbohydrate paradigm
2. A low carbohydrate, higher fat & protein paradigm
Both of these versus the "Western diet". The Western diet is the bad guy, and everyone pretty much agrees with that. They usually mean the 'Pizza Hut-McDonalds-KFC-Dunkin Donuts' diet. Lotsa fat, lack of veggies, and lotsa simple carbs. My favorite!
The choice between #1 and #2 is the issue. On a popular level, if you want to read about #1, any of the Dean Ornish books explains that point of view. If you want to go for #2, any of the "Paleo Diet" books deals with it. Example: 'The Paleolithic Prescription', S Eaton, et al 1989.