For #1: the point of #1 is that body shape and insulin levels are not being considered. That point specifically only matters for weight gain/weight loss. In regards to differing energy expenditure for digestion for one food vs another, I would guess that that is a level of detail the average person would not spend their time investigating.
For McD's vs home cookin, calories in/calories out still holds to be true. So, if your exercise levels are the same, then you will end up weighing approximately the same after both diets. However, lean body mass, body fat percentage, your overall health and the effect McD's has on any diseases you are fighting/trying to prevent will likely be different based on the quality of your diet and it's macronutrient distribution.