As someone who just lost 35 pounds through clean dieting:
All calorie/portion numbers on packaged food are off by 10-20%. I set MyFitnessTracker to 1.5k calories (deficit for my build) and for weeks nothing would budge - even with strict portion control and weighing everything, plus 800 extra cals spent through exercise.
Once I went to "1250" calories, I started losing weight. Went from to 205 to 175 pounds.
With packaged food I mean anything like cream cheese, various sides, etc. - not pre-built meals (I assume those would be off by 50%).
What weighing your food really does, is reveal how shockingly little you actually should be eating. I switched to small plates for all meals, as using the normal large ones was pointless and slightly de-motivating.
But yeah, it's just calories. No matter what you eat.
Another more sensible explanation is that the calorie theory is fully wrong and unscientific, despite using numbers and measurements (it sounds very mathy though)