The simple solution I see?
Food works on a day by day basis. Once you eat for a day you don't need to eat again. All food give as certain amount of action points of recovery from working hard or bunny hopping to much. After you've used up your food you can chose to eat again to quickly recover your stamina, but its not required. Simply resting will do the trick.
Food has a range of values:
Tasty Paste: Produced by the Ark, you can get it from any vending machine along the base of the Ark itself by scanning your arm. You can even stock up on it a week at a time. The paste kind of like Twinkies in that it never goes bad but the only thing it does is sate your appetite and you might go insane from eating the same thing day in an day out. You eat it, you get back what you started. Your fabricator can even make it by randomly absorbing a bunch of foods and congealing it. No need to think about it.
Base food: You haven't cooked it, not very appetizing but you find in the wild. It will sate your hunger but you body won't run well on it. You don't get your base amount of action points back. But hey you aren't hungry any more. You can however turn what you've found into crops, or in the case of bambi... animal husbandry. All farmed food is this until its properly prepared in some way. In a pinch it will help but if you can find enough of it, your better off just making tasty paste. If you have right tools... see below.
Prepared Food: Whether you cook it or mix it with other items, prepared food does better than Tasty Paste and far better than base food. You can't stock up on it as much but each recipe has its benefits that might add to a play style. Some speed up skill game, other increases damage output, or you recover your stamina faster. Its all different. To make prepared food, you follow a recipe or make your own and prepare it using the right tool or element.
Better farmers make better food with higher outputs when its prepared but its entirely optional. A person can just chose to eat tasty paste their entire life.
With higher skills however that can turn growing crops into pharmaceuticals or something, Genetic engineering attributes acquired from crops, researching and exploring into things can be turned into pills. The simple multivitamin then enhances prepared food outputs. Or you can get a skill enhancer with some serious drawbacks or withdrawals.
Hell a ship having a dedicated chef or even a few soldiers with cooking skills could up their efficiency and output. It would really push to multicrew setting.
Personally when I make my ship I'm going to want to include a biohab to grow stuff in.