Nope, I understand your point, you're just still wrong for a pile of reasons that either I've been unable to express sufficiently clearly, you've been ignoring, or some combination thereof.
No one is suggesting that there's no thermodynamics involved. The objection is to using "thermodynamics, duh" as an argument. I generally encounter this in the stronger form of "the only thing that matters for weight loss is consuming fewer calories than you burn, because thermodynamics." That's obviously puerile. However, I think even in your more constrained (and better supported) usage here ("if you burn more energy than you eat, you will lose weight") it is still the case that you need to know other things about human biology; further, you need to know many more things to determine whether losing weight that way is advisable (even before incorporating the many physiological or psychological things that might mediate difficulty), which is the bit that actually matters.
These "many more things", we do have quite a bit of evidence regarding. But that evidence needs to be incorporated into the arguments to make the arguments meaningful.
Ok. I think I get your point now. I just don't agree.
> it is still the case that you need to know other things about human biology; further, you need to know many more things to determine whether losing weight that way is advisable
I believe that there are times when you need to be pragmatic and act before you know more. You might not be sure that losing weight (or that most obvious way to loose weight) is best for any given person but it's still an adivce they should take if they are overweight.
Just like it's a still good advice to excercise even if you are not perfectly sure that excersising won't kill you. You can take position of "I'm not sure. I better stay on my couch till the data comes in, indicating that it's healthy for me to run a bit." but that's not wise. You can't put yourself into stasis before you are sure if it's a good thing to eat less than you burn. Your life goes on and you need to act on incomplete knowledge you have so far.
TL;DR
I just don't agree that acting on "Do what physics tell you, ought to lower your weight." is worse than acting on "We need to learn more about our biology before we can do anything successful about our weight."
We knew plenty more than "thermodynamics" about losing weight before we knew about thermodynamics. I'm not saying "we need more study before anyone should make any changes to eating habits" - of course we need to operate off the best understanding we have (we certainly can't refrain from eating until we know everything :-P). My point is that reducing things to "thermodynamics, duh" is not doing that.