The first study says "[the low carb diet] involves limiting carbohydrate intake without restricting consumption of fat and protein", which means calories aren't controlled for at all. Only carbs are counted. The second study has the same problem, read the methodology section.
Please, link me to "dozens of studies" that refute the link I provided above that: 1) have calories controlled in both groups 2) account for the non-permanent water weight in low carb diets and 3) find statistically significant differences in weight loss vs a regular calorie-restricted diet. You won't find a significant amount, if any.
Your second argument is a really common one and I have never understood it. Agreeing that calorie management is all that is needed for weightloss DOES NOT imply that calories are equal. Calories being equal is not a requirement for counting calories. I understand the concept of TEF and that there are several other factors that can impact what the "effective" calorie amount of foods are. I understand that the human body is incredibly complex and there is no formula for accurately determining an individual's calories.'
But none of these things realistically matter for counting calories as a tool of weight loss. You estimate your calorie intake using one of several googlable methods, then you adjust your intake over time to hit your desired weight loss rate. Any personal variances your body has or any dietary habits you have just get accounted for in the amount as you adjust it.
