When your body is breaking down simple carbohydrates, it causes your blood sugar levels to spike, and during this period you're packing away more fat than you would otherwise. Combined with a sedentary lifestyle it's really bad. It does matter where you're getting your calories from.

This is why poor people have greater obesity problems than the rest. Potato Chips, white bread, pasta, and of course sugar feature prominently in their daily calorie intake, these are the cheapest calories you can make a diet out of.

None of that matters, it's like jitter on a clock line. The timespans we are talking (months), these differences vanish.

I'm sure there are tons of intricacies in how metabolism works, but glycogen storage in a human is about 2000 kJ. Once your deficit surpasses that (and we'll happily allow a multiple to account for any error here), your body will either consume fat or you'll experience actual low blood sugar and drop dead.

The point is that there's a whole lot of complexity hiding behind "calories in" and "calories out". The behaviors of eating, the psychology and physiology of feeling full, of being active, exercising, etc are all very complex. The simple equation is hiding immense complexity.