Address the core issue first before arguing about minutiae. The emphasis on relatively low impact factors is especially unhelpful and unhealthy because people latch onto all these discussions as justification for why they can’t lose weight. Sure, an obese person might have a low metabolism[1], but if they eat 3500 daily calories and live an entirely sedentary lifestyle, those are probably the major causes.
[1] But they don’t. Study after study have shown that obese individuals have high metabolism because metabolism is tightly correlated with total body mass.
Constantly talking about genetic predispositions, obscure metabolism suppressing viruses or gut flora does about jack shit to help people lose weight.
Your body doesn't care how the calories go out. If they're gone, they're gone. If you eat 3000, but crap out 2000, your body doesn't say "Yeah, well, that's not how you usually get rid of calories, so get fat."
Just because our methods of recording aren't perfect doesn't mean that the core idea is wrong.
Also this is still calories in, calories out.