If all calories are equal, there's no difference between the body of someone eating 2000 calories a day of lean protein, vegetables and whole grains, and someone eating 2000 calories a day of deep fried carbs and a few vitamin pills..... right? Right?
o.0
The whole equal calories argument is silly. It's never held true and it's never been real science.
o.000
The idea that one loses weight by expending more than you consume is silly also.
o.00000000
So you seem to be tying together two arguments:
1. Calories are not the only characteristic of food which plays a role in how what we eat effects our body (true).
2. Calories deficits/surpluses don't play any role in whether people gain or lose weight (false).
It helps to prioritize the order of magnitude of effects. The two biggest factors determining whether and how much weight person X will succeed at losing on a given diet are (1) the deficit in calories between what they consume and what their bodies burn every day and (2) the degree of satiation the diet produces.
As others in the thread have talked about, a 1,500 calorie diet is going to produce a lot more weight loss if it leaves you feeling full than if you're painfully hungry all day, because in the second case you're much more likely to cheat, and also more likely to give up on the diet faster.
Foods are pretty interchangable for factor #1, but not for factor #2. If you have food that is satiating enough, you don't have to personally worry about tracking calories because you'll just tend to eat fewer calories than your maintenance requirements anyway (this is how high fiber, high produce diets tend to produce weight loss). There are other ways of tricking your body's hunger response like the high fat "ketogenic" diets which where all the fad a couple of years ago, but again, if you look at how many calories people are actually eating on those diets, after the first week of dramatic weight loss (produced by using up all the glycogen stored in your liver so that you body needs less water to keep the glycogen dissolved in), again the weight loss becomes a matter of calories in, calories out.
Now there are plenty of second and third order factors that are also statistically significant (the energy it takes to digest different kinds of foods, that some people tend to feel like they have more energy when they eat more, so they move around more and burn more calories, while others don't feel this response so their calories out doesn't increase much in response to an increase in calories in, all sorts of hormone signaling cascades), but none of that negates the critical importances of the two factors described above.
Anyway, this is a long winded way of saying that yes, if you eat substantially fewer calories than your body requires, you will lose weight.
The correct observation that there are other factors which determine how likely you are to successfully stick to a diet where you're eating fewer calories than you're using, and that the precise number of calories your body needs is a dynamic number rather than a static one doesn't make the statement above any less true,
or any less scientific.