Why do skinny people live for shorter than the norm even though calorie restriction extends life expectancy?
This is an interesting point you raise, and as the study you linked to states, "the link between physique and life expectancy is not clearly understood," which is certainly true at the moment. The relationship between BMI and lifespan in humans is a very different story to controlled dietary restriction in model organisms.

Dietary restriction is defined as "undernutrition without malnutrition" [1], and by definition model organisms live in controlled environments. In contrast, humans have confounding factors that may reduce weight and health (for instance smoking status, early-life diseases, malnutrition, etc) that are not modelled in these experiments.

In addition, the relationship between BMI and mortality is complicated in older humans, known as the 'obesity paradox'; overweight and obese elderly hospital patients have a lower mortality risk than low-normal weight patients [2]. There are a number of hypotheses regarding this, but the favoured one appears to be that the association is not actually paradoxial, but that higher BMI only appears protective because losing weight is associated with many diseases of ageing, so after accounting for many of these confounding factors (e.g. dementia, cancer, etc) high BMI no longer appears protective.

Therefore the study you found only appears to be contradictory to the dietary restriction experiments; in human populations the situation is much more complicated. Additionally, there is conflicting evidence as to whether dietary restriction even works in primates [3], let alone in humans (the largest effects are observed in worms and drosophila). 




Weindruch et al. The retardation of aging in mice by dietary restriction: longevity, cancer, immunity and lifetime energy intake. (1986) J Nutrition; 116(4):641-54
Yamauchi et al. Paradoxical association between body mass index and in-hospital mortality in elderly patients with chronic obstructive pulmonary disease in Japan. (2014) Int J Chron Obstruct Pulmon Dis; 9:1337-46
Maxmen. Calorie restriction falters in the long run. (2012) Nature; 488, 569