I think that might be limitation of animal models, though. At least in the article, it doesn't say anything about whether or not they forced the animals who were fed a non-restricted diet to exercise. In order to isolate the "caloric consumption" variable, I'd want to see a study that compared the same net calorie consumption (food - exercise) on animals that had a sedentary vs moderate vs vigorous exercise routine. Without that sort of study, I don't think it's valid to conclude that caloric restriction has any benefits.
This has a lot of potential impact on what we consider healthy. If the caloric restriction advocates really are correct, then marathon runners, bodybuilders, and powerlifters are putting themselves at risk of an early death much like morbidly obese people or smokers. The average fitness junkie probably consumes significantly more calories even than the average obese person, but they end up burning off those calories through exercise so they appear fit and healthy. If it's true that the metabolism kills, we should be actively encouraging people to not do that, to instead limit exercise to 30-60 minutes per day of moderate cardio so that they maintain a healthy body weight while restricting calories.