You have it backwards. Malnutrition can lead to impaired growth and lower bone density. But that doesn't automatically mean that lower bone density and lower stature is evidence of malnutrition. For all we know the measured difference between test and control was much smaller than the standard deviation.
Also the list you posted contains substances that our body produces ourselves so we don't need to get these from food (e.g. Creatine)
You are conflating study confounds with malnutrition. Lower stature and bone density is in fact clinical evidence of malnutrition. It is possible that the study cohort simultaneously suffered some other malady like radiation poisoning, but it is unlikely they all suffered maladies resulting in the same symptoms. I think the study design is sufficient to rule that out. It is certainly as rigorous as any other peer-reviewed nutritional study.
Also the list you posted contains substances that our body produces ourselves so we don't need to get these from food (e.g. Creatine)