Each ingredient has hidden effects to determine the result of a cooking. These effects are different than the ingredient's effects when eaten individually, and are not shown in-game.

List of cooked effects here (ignore food values): https://wikizet.com/corekeeper/en/Cooking

To calculate the final result:

• Combine the effects of both ingredients together
• Permanent max health boosts are additive, you can never lose any of them by cooking
• Any other effects are not additive, only the one with highest value is used
• Data for food value doesn't seem to match in-game, they are higher than the one listed there. There might be other factor at play with food value

I don't have the skill to make rare food yet, so I can't confirm how they work, possibly another effects and/or multiplier.