Concerning yourself with highly complex reactions that could happen between foods, when we aren't even sure how/if those reactions happen is effort spent unwisely, whereas calorie counting has a definitive effect and even if those combinations can hamper or help you, even by ignoring them, you still have the overall desired result.
I find that, as a model, calorie in - calorie out works well, even if at some future time we would discover it's not fully accurate.
This isn't necessitated at all. There's no mystery as to what overlaps between what the most successful food regimens prescribe today: cut sugar, cut refined foods, eat more vegetables and eat real food.
Counting calories is important when it comes to weight management, but optimal health does not stop and start just at BMI. You might be thinner on a calorie-restricted junk-food diet, but you won't be healthier. Your insulin would spike all the time, you'd be nutrient-deficient, etc.
All of which to say, you'll be making the task of losing weight easier just by switching to healthy foods, which you should be doing anyway. It's not "complicated", it doesn't need to be politicized.
> Plants, Fruits and Water
Also fungi. And fruits are plants so do not need a special mention.
Some would say meat can be "unprocessed", but its not part of the WFPB diet that I mentioned earlier and it known for it's health (obesity reversing) benefits. To the contrary.
The combination of nutrients in food can have a large effect on the efficiency of nutrient extraction in your stomach and gut. For example, when you consume alchol and a meal afterwards your body will store more fat than if you'd just taken a (slightly larger) meal. This is because your body will prioritize burning the acetate and alchol over anything else (including carbs, fat and protein). Other foods or chemicals might have effects on the resource burning allocation of your body.