Most stock recipes are telling you how to produce the "ideal" - a perfectly clear stock free of impurities and fat. Which is nice for soup and some sauces, but yes, the fat is great too!
I like to separate the fat off only so I can cook with it separately from the stock portion. In fact, I often throw extra chunks of fat into the stockpot to render while the stock simmers, and end up with several inches of fat on top of my stock. Using stock as fatty as that would be very unappealing in a soup or something like risotto or sauce where the fat would "break" from the emulsion and form big puddles of grease.
If your stock only has a thin layer of fat on top, I would leave it. Otherwise, skim it and use it for sauteing , roux, etc.
I don't consider myself a TF expert, but it is my understanding that it is not the TF cookbooks or websites that tell you to remove the top layer of fat,rather the more mainstream ones that are still overly concerned with fat.