So, yes and no. That's why I said "primarily." It's wayyyyy more complicated than calories-in vs calories-out. But 90% of it does come down to that. More importantly though, you need to define what "calories-in" means.
I like to think of a silly extreme. If I drink a gallon of gasoline, I've technically consumed what, a billion calories? But I won't gain a single gram.[1] Why? There's no metabolic pathway to convert gasoline to ATP.
If you take that silly example and moderate it, you can see how different factors, including genetics, gut flora, adaptation, etc could affect what is even processed and thus part of the "in" variable.
More concrete, well known examples:
- If you consume 5000 calories of just protein, the metabolic pathway to convert to lipids is extremely inefficient. You will mostly excrete the excess.
- Similar with pure ethanol. If you drank just alcohol (and nothing else), there is no metabolic pathway to convert this to fat.
- Even carbs. If you just ate 5000 calories of pure carbs, de novo lipogenesis (metabolic pathway for carbs -> fat) is rather inefficient. You will gain weight but less than the 5000 - expenditure. A lot of it is burnt off as heat.
- Sadly, for ketoers: the dietary fat to lipid pathway is extremely efficient. Almost 90% of excess will be stored as fat.[2]
See a pattern here? The reality of the typical diet is that we don't just eat one macronutrient. We mix them. And specific ratios are what make food hyper palatable and thus so easy to overeat. Once you start mixing things up, it basically - and I mean basically - comes down to calories in vs calories out.
[1] In fact, I would likely die.
[2] As another commenter mentioned, there was one guy who just ate fat and well in excess of his BMR and apparently lost weight. I'm skeptical, but could believe it simply because it follows the trend: consuming just one can "bend" the rules.