I notice negligible changes otherwise, I think that part is the coming down to genetics micro biome and what you're eating.
>That suggests that for me, not all calories are calories.
That's way too deceiving for newbies to read cause, yes but no. Once you're out of obesity body fat ranges and into just higher than normal that's when you can see benefits from the aggregate of the tiny changes. So looking at that low level helps alot, however if you're cutting by 300-500 calories that's plenty of wiggle room to account for your metabolism handling fat better than carbs and vice versa especially when starting out.
If one not weighing everything and measuring it will make it seem much more like a calorie isn't a calorie because it's much easier to accidentally 'over eat' enough to change your hormone response to eating. Like cooking oils, they could be adding 200+ calories to your meal without you realizing it. Carbs wise a bowl of pasta is great for you but one extra scoop and boom there goes 100-200 calories, changing your average cut amount from maybe 300-500 to 100-200.
You need consistency to communicate with your body those fluctuations is what causes gains of fat.