The game does not provide guidelines for this.
D&D 3.5 is not a "life simulator". It is a game whose mechanics largely involve abstracting combat against fantasy monsters. How a character handles the digestion of magical food is a detail the game simply does not address. In fact, the game doesn't seem to consider food an important topic in general, it often being handwaved away. Digestion is way below the simulation threshold - unless it has to do with fighting monsters.
Nevertheless, you are asking a question about a situation that can come up. People can and always will come up with questions the game can't not address, given the open-ended nature of RPGs.
In D&D, such questions are mostly answered by the DM. The DM makes some kind of ruling, and the game continues. If you are the DM in this situation, I suggest you go with whatever ruling that you think is...
- most likely to improve fun at the table right now (is it funny to have a Wizard with a suddenly-rumbling stomach?)
- most likely to improve the story being told (could a Wizard dying of magically-induced malnutrition be a good plot point?)
most likely to enrich/improve the players' experience of the game world (does it being possible for any 1st level Psion to create food from nothing have an odd effect on the setting?)
... and so on. In any case, you're going to have to make a decision for yourself. The game doesn't help you.
Like the other answer says, there's no system for this in the pathfinder rules. So here are a few house rules you could use. I would start by inverting the rules for starvation and thirst.
As you get dehydrated, you make successive constitution checks and start taking non-lethal, and then lethal damage every hour. Further, characters who are starving or dehydrated become fatigued. So, being well-fed should invert these effects in some way.
Here's an example status effect I've come up with that could implement this:
Nourished
A nourished character can run as if she possessed the Run feat, and is granted a
+1 circumstance bonus to Strength and Dexterity based checks, as well as a +4 circumstance bonus vs effects that cause fatigue or exhaustion. Becoming fatigued or doing anything that would cause fatigue removes this condition. Otherwise, it fades after one hour.
And also a potential implementation of Profession (Cooking)
Profession (Cooking)
You are skilled at preparing exceptionally nourishing meals.
Check: Preparing a meal has a DC of 10 (for a decent meal), 20 (good meal), 30 (extraordinary meal), or 40 (legendary meal). You need ingredients, and a suitable kitchen or equivalent work space. Without a proper kitchen, you take -4 on your cooking check. Cooking without ingredients is impossible.
Decent Meal: Pretty standard fare. A decent meal grants the nourished condition
Good Meal: A good meal, the kind you could expect to find in a particularly expensive restaurant or luxurious inn. In addition to the effects of the nourished condition, a good meal grants a +1 circumstance bonus on fort saves for the condition's duration.
Extraordinary Meal: An incredible meal, the like of which most people will experience only rarely, unless they are quite wealthy. In addition to the effects of a good meal, an extraordinary meal grants 1d8 temporary hit points.
Legendary Meal: A meal of legendary quality. As word gets around of your skill, kings will fight to have you in their kitchens, and beings from other planes will seek you out to experience your masterful creations. A legendary meal grants the nourished condition, as well as a +2 circumstance bonus to all saves, and d8 + (Cook's HD) temporary hit points. Such a meal is so good that creatures who taste it can't bear the thought of dying without tasting it again.
Action: Preparing a meal takes one hour, although a particularly intricate or important meal may take longer, at the GM's discretion.
Try Again: Yes, but every time you prepare a meal any ingredients used are consumed.
And finally, some sample items
Ingredients
Basic Ingredients: The bare necessities required to create a meal. Price: 1s. Weight: 1/4 lbs.
Extravagant Ingredients: Very extravagant ingredients. Grant a +2 circumstance bonus to a Profession (Cooking) check made to create a meal. Price: 15g. Weight: 1/4 lbs.
Legendary Ingredients: Incredibly hard to find ingredients, of legendary quality. Grant a +5 circumstance bonus to a Profession (Cooking) check made to create a meal. Price: 500g. Weight: 1/4 lbs.
Tools
Cooking Kit: Basic tools required to cook a meal. Price: 5g. Weight: 5 lbs.
Kitchen: This kitchen is used for cooking, and provides a +2 circumstance bonus on Profession (Cooking) checks. It does not provide any ingredients. Without this kitchen, a character with the Profession (Cooking) skill is assumed to have enough tools to use the skill but not enough to get the +2 bonus that the kitchen provides. Price: 200g. Weight: 40 lbs.
Best Answer
Generally, I think you're on the right track to try to enforce some mechanical consequence to the choice of lifestyle.
I think the right choice is to use the second option more often than not. In specific circumstances (especially in social interactions), certain kinds of lifestyles should grant advantage or institute disadvantage. For instance, if you're a stable sleeper, and have to go in front of the Lord of the Town, you're likely to have disadvantage on all your checks. But the inverse is also true, if you're a hotel dormer, and don't make allowances, you're going to have disadvantage with the slumlords etc.
Again, I would make sure there are opportunities for him to...essentially pay...to remove some of this. For instance, if he's been slumming it for a few weeks, he could go to a bath house, pay a GP or two to get a good bath and get cleaned up. I might still harm him if rumors are floating about, but at least he'd look like he was supposed to be there. In other words, it shouldn't be a mechanical penalty that is permanent or robs the player of his agency. Just one that he has to work around occasionally.
As far as awarding inspiration, this should be very much tied to the BIFT (Bonds Ideals Flaws Traits) of each character rather than anything specific to their lifestyle. However, if they are (for good reason) entering a lifestyle that is in character, but conveys some kind of situation disadvantage (for instance, a Hermit staying in the woods, even if it means he misses something important in town).
Basically, inspiration is a reward for taking consequences for staying in character. So if your PC, within their character, decides to slum it, but then has disadvantage with the town noble the next day. That's actually cause to award inspiration, rather than the converse (rewarding them with inspiration for living an out of character lifestyle).