Compared to the other diets, the low carb diet produced the smallest decrease in (resting and total) energy expenditure, a greater decrease in leptin (perhaps indicating a greater decrease in leptin resistance), better insulin sensitivity, lower triglycerides, and lower PAI-1 levels. These are all points in favor of the low carb diet in my mind.
Compared to other diets, CRP levels were higher in the LC group. However, all diets produced a decrease in CRP levels compared to baseline (which was 1.75) and ultimately the difference between the 3 diets was hardly significant (.78, .76, and .87). I'm critical of the author statement that low carb diets may increase CRP; this depends on context. According to the American Heart Association a CRP below 1 is considered "low risk". The low carb diet produced a CRP of .87.
The cortisol reading was interesting because it actually did increase in the LC group both compared to baseline and the other diets. I suspect cortisol increased to support gluconeogenesis; this effect was likely accentuated due to the high protein intake (30% of calories).
And as some have stated, diet quality may have had an effect. I suspect low intakes magnesium, vitamin C, and other nutrients more likely to be lacking in the LC group could have produced such effects on cortisol (and CRP).