Shouldn't you have to disprove the obvious explanation (that it's calories consumed that leads to obesity) before we should jump on board with wilder theories?
I read the link you posted about the keto diet, and it seems to all be about how it's better for you with regards to cholesterol and glucose levels. It doesn't seem to negate the idea that weight is still simply related to calories consumed.
(I recognise there are exceptions, i.e. thyroid/hormonal problems).
That's like saying good, on-budget software projects are simply related to number of lines of source code per day. Obviously, you won't get anywhere on zero lines per day for months on end with a 12-month project. Not as obviously, you and I know there are far more other factors to consider than this layman's level metric.
We're at that layman's understanding stage with our grasp of human metabolism. Counter-intuitively, Jason Fung among others have discovered that steady caloric restriction has worse body fat loss long-term outcomes than zero-calorie straight fasting over a span of time of >24-48+ hours, even if the net calorie loss between the two methods is exactly the same.
We don't really know at the molecular biology level why that happens. We have some good hypotheses and experimental evidence about which hormones are involved in this counter-intuitive result. Even weirder: when you break the fast, if you break it by going onto a low-carb, high-fat diet, your odds of consistently keeping the weight loss off go up. Again, we don't really know why at the nuts and bolts molecular biology level.
There are even claims by people on low-carb high-fat diets that they eat more than their computed TDEE as tracked by something like MyFitnessPal's nutritional database, and yet they're still losing weight. I've noticed this tends to be reported more by people who are quite obese; I've yet to see someone who claims this who is in the normal BMI range. I haven't seen any double-blind studies attempting to verify this yet; would be nice if MFP could crunch numbers to share.
At a very, very gross global population level, you are absolutely right that it is CICO (calories in, calories out). Digging deeper though, there is a lot we simply don't know enough about. For very obese people, other hypotheses and mechanisms seem to be helping at least a good number of them to the point where the /r/keto board is quite popular, and just repeating CICO in the face of this empirical evidence doesn't advance human knowledge. We should be saying instead, "hm, that's not what I expected, why is that?"
I read the link you posted about the keto diet, and it seems to all be about how it's better for you with regards to cholesterol and glucose levels. It doesn't seem to negate the idea that weight is still simply related to calories consumed.
(I recognise there are exceptions, i.e. thyroid/hormonal problems).