The wiki on cooking and recipes says the total calories in food doesn't change when the food is cooked. This is not accurate to real life.
Cooking food increases the food's net metabolizable energy (NME) — the calories your body can actually extract — by breaking down cells in advance, reducing your digestive effort. This is the main reason humans cook food. The extra energy we get from our food by cooking it is the reason we can have huge energy-consuming brains and small stomachs relative to other creatures. It's a big difference, and it makes sense to include this in a simulation of human metabolism of food.
NME bonus calories vary by individual food. By data from nutritionists: Cooking meats typically adds around 20% to their NME. Berries are also close to 20%. Cooking starchy vegetables (such as turnips or reed roots in the game) adds about 50% to NME calories, and processing and cooking grains adds 200-300% compared to eating raw grain.
Some players have commented in the past that making soups and especially porridges doesn't seem worth the effort for the food value you get. The numbers above show that those are the foods most affected by neglecting NME, so to the degree that's a real problem, this is a good explanation for it.
My first suggestion is to just expose a "nutrition multiplier" parameter for each recipe in cooking mod text files. That way I can do all the work for my own idea, and make a NME recipes mod for myself and the players that want to try playing with these changes.
Or if you decide this is a good feature to add for everybody, adding bonuses by cooked food category (20%/50%/250% for meat+berries/veg/grain) would be a simple change that is mostly accurate to real life. Or to be more cautious against upsetting the current game balance, perhaps cut those values in half as a starting point, then tweak for balance.