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bentarm comments on Minimum viable workout routine - Less Wrong
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Well, calories in, calories out is trivially true. As far as I can tell, all it actually says is that the amount of food that you store as muscle mass/fat is the amount of food you store as muscle mass/fat - it's just that it is not easy to measure the "out' part.
I agree that it is a ridiculous over-simplification. As Taubes puts it, saying that obesity is about over-eating is about as useful as saying that alcoholism is about over-drinking.
I don't want to argue about what a cause is, but you can become obese for other reasons than over-eating, for example if you develop hypothyroidism you often times become obese even tough you have not increased your food-intake or exercise less than you use to.
As the laws of thermodynamics, yes; applying it to fitness is intractably hard, and attempts to approximate caloric intake/expenditure for that purpose have all been intractably difficult or laughably bad. That's why it's not something that should be told to people just starting out. They'll inevitably use it incorrectly and get shocked when starvation causes their body's metabolic rate to plummet.