On a purely formula level - yes, this is how our bodies work. However, many, many nutritional deficiencies can mess with that, making our metabolisms slow down and stop burning efficiently. So this can make a difference in how many calories your body burns to keep you going, which can effect how much weight you lose. Eating a balanced diet can help you maintain your metabolism, which will allow you to burn the most calories you possibly can in a day, leading to greater losses.
Also, to complicate matters, most people find it impossible to stick to a plan of eating junk food, even with the calorie control. The reason? Protein and fiber (found in healthy stuff, like grains and veggies and lean meats and dairy) help to keep you full longer, while refined carbs (white flour, white sugar, white rice, corn syrup, etc) actually make you hungrier, faster, due to hormone changes. So eating a diet of healthy foods will help you stick to your plan more easily and for longer, which leads to better results over the long run.
My personal experience - I could never stick with a plan that was "junk food" based, even when doing my most diligent calorie counting. I'd always give up because I was so hungry! Only when I started eating whole, healthy foods did I get a good, consistent weight loss.
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