I think they are saying the caloric intake was measured, but they didn’t distinguish between what kind of food the calories were coming from:
> The participants were monitored for two weeks. Their food intake was measured with an isotope-based technique called the doubly-labeled water method, which assesses energy expenditure based on the difference between the turnover rates of hydrogen and oxygen in body water as a function of carbon dioxide production. Their physical activity was measured using an accelerometry-based motion detector.
Also regarding the specific food choices:
> The team is now expanding its research, including studies that include these measures. They also plan to look at genetic differences between normal weight and healthy underweight individuals. Preliminary analysis suggests single nucleotide polymorphisms in certain genes that might play a role.