I don't know about any sort of rule of thumb that can be applied to digestion efficiency. I think it will also depend on an individuals metabolism, if you are hungry(energy low) in the first place etc.

If you have starved yourself prior then your body is liekly to absorb more nutrients and if you've just had a Sunday roast and are topping up with dessert then this will turn to fat. Which is a shame becuase if you body just passed through 100% food if you were full, the world would be a happier and thinner place

1gm Fat = 9calories
1gm Protein = 4cals
1gm Carbs = 4cals

I thnk you are right though in assuming there are foods that are harder to extract nutrients from........