Cantrips are powerful, in their own way
As the PHB says, cantrips are "simple but powerful spells that characters can cast almost by rote", and:
A cantrip is a spell that can be cast at will, without using a spell slot and without being prepared in advance. Repeated practice has fixed the spell in the caster's mind and infused the caster with the magic needed to produce the effect over and over.
Already we can see that cantrips can have more profound effects on the game than other, leveled, spells by virtue of their being cast at will and repeated ad infinitum (if not truly infinitely). It is incorrect to claim that a cantrip cannot duplicate some of the effects of a higher-level spell or even that it cannot be more powerful in some ways. The Gust cantrip, for example, is less potent than the second level Gust of Wind in that it has a shorter duration and can affect fewer creatures. And yet it has a similar effect - it creates a wind that blows things away. In some senses it is actually more powerful - the cantrip can move objects, while the second level spell cannot! Thus we can reject out of hand the argument that "prestidigitation cannot create nourishing food because create food and water does."
If cantrips in general can be powerful, Prestidigitation (and its lesser cousins Thaumaturgy and Druidcraft) can be particularly powerful because of their flexibility and the range of effects they can produce. Prestidigitation can be a solution to many potential problems. It is a spell for creative players. When a player selects Prestidigitation as a cantrip, it is time for a mini-Session 0, a conference between the player and DM about what particular effects will be permissible, and which not, in their game. If a DM does not want to let Prestidigitation have a particular effect in their game, it is their table and their decision - but they should be up front with the player so that the player can make an informed choice about the value of the spell to them.
What can you make with Prestidigitation?
As Groody the Hobgoblin points out in their answer, the trinkets made by Prestidigitation are, by definition, non-magical, so forget your magical regenerating cupcake. Let's focus instead on your bag of seeds. "Seeds" provides me with all the leeway I need as a DM without inventing rules or rulings or nitpicking spell description language. If I don't want you to be able to feed yourself with Prestidigitation, I can simply declare that your seeds are avocado pits. If I am okay with you using the spell as a food source, your seeds can be cashews - heck, they can be roasted and salted cashews. Both of these are possible following the RAW description of Prestidigitation creating a trinket temporarily.
Can disappearing seeds be used to feed you?
Yes, the trinket made by Prestidigitation disappears at the end of your next turn - meaning you have all of your current turn and all of your next turn to interact with it. If I hand you a bag of cashews and give you twelve seconds to eat them (or even six seconds if for some reason you are not permitted to use your free object interaction on the turn you made the bag appear) a substantial number of them won't be cashews any more, they will have been changed into something else. They won't be seeds; they will be food that you have eaten. The uneaten seeds disappear, of course - that's in the spell description. The seeds that have already been eaten, however, that have already been changed into something else and have interacted with your body - why should their new form disappear down to the molecular level? That is not in the spell description. I can use Prestidigitation to make a vial of water, and use the water to snuff out a candle - does the candle re-light itself after six seconds? Do I have to remove any trace of its chemical interaction with the flame as if it had never been there? I can use Prestidigitation to make "an ancient arrow of elven design" (PHB trinket 91). If you shoot that arrow at a foe, does the damage disappear along with the arrow at the end of my next turn? Not at my table. Yes, the trinket disappears, but before it does so it is permitted to make permanent changes in the world. When you eat the seeds, they are no longer seeds - they have become food, and you have still eaten a mouthful of food even after the uneaten seeds disappear.
You might be tempted to think that "because digestion takes time, even the seeds that were eaten must have their nutritional value removed." This seems like an appeal to a modern understanding of metabolism - so we should immediately be suspicious of the claim. Remember, this is a game in which a mortal wound will either kill you or no longer affect you after 30 seconds at most, in which wounds that are anything short of killing you will be completely healed through rest alone after 12 hours at most, but in which a person of average Constitution running as fast as they can for 36 seconds can kill themselves with exhaustion. Modern understandings of metabolism must be set aside when the more important goal is what we are trying to accomplish with the rule.
What is the point of this 'realism'?
D&D is a game of heroic fantasy, not a game of biochemical simulation. Does your DM insist on rules for how quickly food passes through you and whether you have to defecate when you are encased in plate mail? Do they worry about whether rainwater spoils your bowstrings? Do they break all your potion vials and oil flasks when you fall down a twenty-foot pit shaft? Do they burn the scroll that was in your hand when you were engulfed in the breath of a red dragon? If the answer to all of these is No, but the same DM suddenly looks up real world biochemical rates of nutrient absorption when you try to feed yourself with the Prestidigitation spell, it is not because they are being realistic. Rather, it is because they do not want the spell to work like that. As DM, it is their game, their world, and it is fair for them to have the spell not work like that. But pretending to you, or to themselves, that it doesn't work like that 'because realism' is a poor excuse, a cop-out to owning up to what they want at their table.
In my traditional combat-heavy campaigns, having a wizard that was barely able to feed herself in occasional but dire circumstances through use of one of her three cantrip slots would be considered clever play. Good on her. If I were running a survival-based campaign, where finding enough food was one of the central challenges, using a cantrip to 'solve' one of the core problems would be game-breaking. I simply would disallow that at the outset. But I would explain the actual reasoning to the player, rather than inventing an excuse about how the powerful magic spell 'can't work like that'.