From the article:
"Milk contains healthy vitamins and minerals that are naturally stored in either water or fat. Because skim milk is made by removing the fat from whole milk, skim milk has more water-soluble nutrients like calcium but lacks fat-soluble vitamins A and D. The FDA requires dairy farmers to add synthetic versions of those lost vitamins to skim milk in order to label skim milk as “skim milk.” Without the fat of whole milk, the vitamins break down in skim milk before reaching consumers. In other words, the FDA manages to confuse American milk drinkers without providing any health benefits."
The addition of vitamins seems to be a useless step (because they break down without fat and do not provide health benefits in the end) that probably costs some amount of money that could be saved by a small scale farm. Also the marketing value of being able to honestly say "100% natural, no additives" etc. is another factor.