Well, there are about a zillion parameters in the human body with complex interactions, genetic & epigenetic dependencies, etc. that we barely understand! Yet we assume that everyone is the same?
I'll tell you where this unscientific belief comes from--
Well first we should explain your unscientific belief that this is in fact what either myself or other doctors are describing. It's not that we believe that people are the same but that people are not significantly different in a number of parameters pertaining to BMR. Just because there are lots of things going on in the human body doesn't mean they all affect BMR significantly. That's where your ideas go wrong.
The other problem with your terribly unscientific religion is that you're not controlling for activity or correcting for the fact that people are kind of bad at determining their caloric intake. Considering this conversation was about me correcting someone who claims they take in 3000-4000 KCals/day and doesn't get fat. You appear to immediately take this as evidence supporting your belief without attempting to correct for the fact that this person really doesn't eat that much, or is under 18 or that they're actually more active. It wouldn't take much error in all those parameters to bring that persons actual intake/weight to conform with predictions made from BMR.
Most discussions of obesity have a heavy bias toward the view that people simply choose to be pigs.
This is actually unrelated to what either the OP was talking about and I think that "most discussions" needs to be qualified.