This is not in conflict with your point above that nutrients are removed along with the fat in processed milk, that are then readded (e.g. vitamins A and D), but it's important to realize that those single digit percentages refer to fat in terms of weight.

Ignoring the water content of milk, and looking solely at the caloric percentages, the fat ratio is:

Whole Milk: 48% fat

2% Milk: 33% fat

Skim milk: 5% fat

Referring to fat content of foods and beverages by percent of weight is generally not a useful measure for nutritional purposes. By that thinking, if one were to drink a few glasses of water and then eat 1/2 a pound of ice cream, they could claim they had a low fat meal, because the total grams of fat from the ice cream is small compared to the total water weight of the two items they consumed.