Therefore, balancing calories in to Calories out is not so stupidly simple as it seems to the underweight layperson.
What about the previously slightly obese person and currently healthy weight person (by BMI measurement)? Because that's me. And even during the obese period, I never had any delusions about it not being as simple as balancing calories in and out. It was a matter of changing my mindset so that I was actually serious about the work involved.
Are they right that the number of calories you take in isn't exact? Of course. It's even harder to measure the number of calories out. Does this matter? Not in the least. They're good enough rough approximations. If you're trying to match your calories in to your calories out to a net -5 calories, you're doing it wrong. Aim for at least -500. Even if you're wrong by, say, 400 calories, you're still negative -100 and in the long term will lose weight. Sometimes you'll be wrong in the other direction and will be negative even more that 500 calories for that day. Chances are, in fact, that the long-term average will approximate what you're aiming for.