Think of it this way. Let us say the 16GB, 32GB and 64GB versions of iPhone 5 are like 3rd class, 2nd class and 1st class service in a train car. In the early days of American railroads the operators did offer three classes, with the 3rd class at really affordable prices. But the operators wanted those who can pay higher prices to willingly do so. So they removed the roofs in 3rd class cars. People who can afford second class were no more tempted by cheap prices of 3rd class tickets.
In case of iPhone 6 Apple didn’t remove any roofs or cripple it. They decided to add free extras to 2nd and 1st class car passengers for the same money. You can choose to remain in 3rd class but you are not getting free drinks or umbrella.
Assuming the article's #s are accurate, Apple conservatively stands to make $4 Billion by deliberately maintaining the 16GB floor and cutting out the 32GB option. Margins people. It's always about the margins.