I generally agree with your two issues 100%, but one thing I've found interesting about these discussions is that no one seriously questions the fundamental hypotheses involved, that typical diet bears any relationship to long-term health.

That is, it's assumed it does, but we just can't pin it down because of poorly done studies.

My guess is that that's true, but the other very real possibility is that our bodies are designed to process a very wide variety of foods in a very robust manner, such that as long as you're not eating something obviously poisonous, it doesn't matter as long as you're not depriving yourself of something important nutritionally (as in scurvy).

Similar arguments can me made with regard to weight and exercise, although there it seems like the effects are clearer in certain ways (e.g., I doubt anyone would argue that being in shape isn't better than being physically deconditioned).