Something which is probably not true, but is probably not 100% false, and is in line with what you're saying: "These 5 Genes Predict What Kind of Diet and Exercise is Best For Your Body". http://rockstarresearch.com/these-5-genes-predict-what-kind-...
Supposedly, some people lose weight on low-fat diets, and some on low-carb diets. A few can lose weight on either. And most people need high-intensity exercise to lose weight, while a few only need low-intensity.
(I have both forms of genetic privilege, and have never had to worry about my weight.)
I'm also bullish on microbiome transplant for weight loss.
The articles I've seen don't talk about transplants to help people change their weight. Their thrust was more geared towards explaining (or disproving the significance of) measured differences, and detecting differences doctors can recommend the most likely most efficient diet for people with health problems who are currently having trouble shifting weight.
It isn't just varying the food that makes the difference: there is variation by individual as to how certain foods affect the body. There is evidence that it can vary somewhat not just by age and gender, but the results are noisy enough within tightly controlled test groups that it varies per individual. Where there isn't an obvious cause for this such as diabetes, differences in gut microbiome are suspected to be key.
Everything you said is still correct of course. This variation just adds wrinkle to it, but a small enough one that "calories in" against "calories out" is accurate enough for the vast majority of the population (i.e. those without significant medical issues).
If you are aware of this there is nothing wrong with exercising more so you can eat more, just be careful not to bias your diet by making the extra all "bad food" or you risk being the right weight but unhealthy in a number of other ways. These days I run for three reasons (roughly in order):
* Cardiovascular fitness. It is nice to feel healthier than old me ever did.
* Stress. A 30 minutes jogging with good music or a podcast and/or around some nice scenery is a great way to break away from hassle long enough to relax so you can deal with it better when you get back (burning 250 calories while you are doing it is almost a "freebie"). Don't speed run while stressed though, you'll not concentrate and damage yourself via putting your feet in the wrong places, bad posture, or literally running into things.
* Helping to get rid of the extra I've put on if I had a bit of a food bender last week (over the festive week for example) a little faster then I otherwise would.