IIFYM is a layer of complexity on top of Calorie Counting. If Calorie Counting is "Eat whatever you want as long as you eat below X Calories" IIFYM says, "Hit your calorie mark, but make sure you have enough Fats/Proteins/Carbs". It's not shocking that it would work since it is strictly better than Calorie Counting which also works, but its goal is primarily Body Composition, IE becoming leaner. There is plenty of room to improve on top of that by improving the quality of the nutrient sources and managing micronutrients.

This study isn't a contradiction. It just says that micronutrients matter, which is pretty uncontroversial.