> So if for some reason you're in the second one, even though you ingest the same amount of calories, the amount of energy you have usable is much less.
This is technically true but not particularly relevant.
It's quite difficult to be in only anaerobic effort, though (and I'd say pretty ill advised since that basically means stuff like all out sprinting without warmup or cooldown).
Higher intensity effort burns more calories than lower intensity (eg [1]). It's just harder to sustain.
1- https://www.webmd.com/fitness-exercise/what-to-know-heart-ra... )
Thiamine deficiency can cause anaerobic usage for example, without having to do intense exercise. Severe insulin resistance is another one. Cancer cells predominantly use anaerobic burning (Warburg effect). Various blocks at mitochondrial level, such as carbon monoxide, can also drive metabolism towards anaerobic pathways.
You eat less calories, your body might start consuming less calories.
Also, there are two different pathways for using glucose in the body: aerobic and anaerobic. The aerobic one produces 15x more ATP (cellular level energy) than the anaerobic one. The anaerobic one wastes more as heat. So if for some reason you're in the second one, even though you ingest the same amount of calories, the amount of energy you have usable is much less.
So yeah, calories in calories out is true, but it's not really helpful.