An example with an oversimplified diet to illustrate the point I think you're trying to make: You have a diet that's exclusively cake and you've determined that you need 2000 Calories of cake to maintain your weight. That 2000 Calories figure is an estimate and we don't know exactly how much of it we're actually absorbing. In reality, it's actually more like 1800 Calories. Now all of a sudden, you switch your diet to eating exclusively cookies. You measure out exactly 2000 Calories of cookies and eat the same thing every day. But your Calorie estimate is wrong and you're actually eating 2100 Calories of cookies per day. Now you gain weight on this supposed 2000 Calorie diet.

I argue that this doesn't matter either. If you see that you're gaining weight, then it means you're eating too much. Reduce your Calorie target and you'll be back on track. In a real world scenario, you're going to have a much more varied diet than only cake or only cookies, and each item will come with their own measurement errors. But for most people, their diets are varied in a fairly consistent way, so these errors are also consistent on average. If you ever make changes in your diet (e.g. completely cut out McDonald's), you'll change both your estimated Calorie intake and target like in the example above. Adjust your numbers accordingly based on how your bodyweight moves and you're good.

Of course, other ways of dieting are also effective. It depends mostly on what you can adhere to and your goals.