Whole milk: Does a Body Good? or B.S. (Bad Science)?

NPR carried a story being passed around about people drinking whole milk being healthier. Is it a valid presentation of findings?

After they open with a personal story of a mother who uses whole milk, they write: "Consider the findings of two recent studies that conclude the consumption of whole fat dairy is linked to reduced body fat.... [H]igh-fat dairy was associated with a lower risk of obesity."

I do not doubt the studies, but the verbs are key: "associated" and "linked". We must distinguish correlation and causation. This is not a study of causation but an observation. But the italicized "lower" distracts from them.

They write, "It's not clear what might explain this phenomenon." Excellent. They list these two reasonable explanations:

1. " The higher levels of fat in whole milk products may make us feel fuller, faster.... we may end up eating less."
2. "There may be bio-active substances in the milk fat that may be altering our metabolism in a way that helps us utilize the fat and burn it for energy."

That last is a quote from Greg Miller, executive vice president of the National Dairy Council, who may have a vested interest.

The list makes it appear they've exhausted all possibilities. There's at least four(-ish) other possibilities not examined:

1. People who eat less can eat what they want. People who eat too much have to look at caloric content.
2. Some people have better metabolisms (either due to genetic causes or daily habits) and they can eat what they want. 
3. Something not yet considered occurs--something we may never consider.
4. A combination of these and/or other possibilities.

These other possibilities do not mean that the NPR article is incorrect. Rather, it might give listeners or readers a false impression.