Do you have cites to non-incentivized peer reviewed research showing something other than calories? Disinfo runs supreme in this area... Yes, any research short of complete proof is subject to attack but it's a question of comparative credibility. Between bro science and disinformation it's hard to navigate but....thermodynamics has actually been proven.
I used the term "flaws" for a reason and didn't say it was wrong, also I think about it not from a perspective of how to lose weight (which is fairly easy) but from a perspective of how to keep it off (because really, that seems to be the impossible task that no one is showing positive results for).
Much of the consolidation around calories in vs calories out comes down to the studies of long term effects of different weight loss plans and that they all seem to end up at the same, less than satisfactory endpoint. No one has shown significant lasting weight loss with sustained health benefits using a calories in v. calories out model. Most studies have shown short term (6 months-2 years) 5-20# losses, which is really not ultimately what we want.
Thermodynamics is absolutely proven, not arguing that, but for long term weight loss we've also seen that a significant shift in basal metabolic rate occurs (way down) so if the system is so adaptive how do you construct permanent solutions when the body fights everything you do. That adaptation and return to baseline is a powerful force that seems to be present no matter how weight loss is accomplished (medical, surgical, diet, activity).
The problem with research (disclosure, sometimes I am a researcher) is that your results are constrained by your primary research question, your null hypothesis, and your research design. So if your research question is "does A work better than B", positive results only tell you whether A works better than B, and tells you nothing about how it compares to C.
Another example is the research on whole grains. A lot of that came from some of these large scale longitudinal epidemiological studies that looked at groups that ate whole grains as compared to groups that ate refined grains, but no one looked at no grains. So from these, all we really know is that whole grains are better than refined grains, not whether whole grains are actually good (I don't know the answer to this).
I am just super aware of this because in my current job we are doing things that were researched in the 70's-80's, not found to be helpful, but then when the research question was better defined and confounders were accounted for, research in the 2000's revealed benefits. Even well designed ethically sound, peer reviewed research has limitations (if only with the expectation of a p-value of 0.05 resulting in one in every twenty papers being wrong, coupled with a positive results publication bias, it's very possible for well conducted erroneous research to get attention it doesn't deserve).
I know the research, I've read the papers (good and bad) and get the newest research and re-analysis (good and bad)in my inbox on a semi-regular basis. It really is all over the place, and until we first account for the bad data from the 60's, look at some of the unintended consequences of that on brain function (which drives behavior), take into account the effect of trans-fats, and re-equilibrate, I just don't think it's possible to say anything with certainty about significant long term weight loss.