FYI, I'm a professional nutritionist. Not that its a guarantee that I'm right. But the odds are I do know what I am talking about.
Let me give you a very small example. Does vitamin D from food have the same effect on the body as vitamin D from sunlight prepared under the skin? They have different routes of processing. Vitamin D when taken in foods is processed the same way as fats. It enters the portal system, is bundled along with fats and gets stored in adipose tissue. When produced under the skin, it is taken to the liver and kidney vy the Vitamin D receptor and activated to 1,25 dihydroxycholecaliferol, the metabolite which performs all the functions of vitamin D. How does vitamin D from adipose tissue get released? When the fat is burned for energy. But is it utilised the exact same way? Is there a down side to eating it rather than making it? Consider that in 20 mins under UVB you can make over 20,000 IU of vitamin D, but the DRI [Dietary Reference Intake] for it is topped at 200 IU for children and 400 IU for adults. Why? because we don't know for sure that large doses taken orally may not be toxic [there is one weird study from back in the 50s that suggests it may be, but recent research using upto 100,000 IU in rats does not show the same effects]. Epidemiological research suggests that vitamin D may play a role in prevention of cancer, obesity and muscle loss and may have no effect on bone other than calcium transport [which has been successfully circumvented in the absence of vitamin D]. Recent research also suggests that cells other than the kidney [mayhaps even all cells] have the ability to activate 25 hydroxycholecaiferol for their immediate local needs. We still don't know how 25-D enters the cells.
Almost all the vitamin D we get from food is artificially added i.e. it is not naturally present in the food or at least not present to the degree it is after enrichment or fortification. Changes have to be made to make it miscible [example, in orange juice]
So let me summarise:
1.this is an extensively studied nutrient
2. we don't know
-if the oral form is as effective as the one synthesised subdermally
-how much is safe
-how much we should eat
-whether we are eating enough
-whether we are eating too much
-whether it is any good eating it at all
-what are the effects on the body
-what does the body do with it
-whether it is a causal factor in chronic disease
-whether eating it will help prevent these diseases
-whether the previously known "facts" about it [effects on bone] are entirely valid
And this is only with relation to the vitamin. I haven't even gone into its interactions with other nutrients. And this is a relatively minor micronutrient that we can get from the sunlight if we don't take enough of it. One we know of. We haven't yet identified all the components of food. So any suggestion that we can artificially tailor it to our needs is an argument from ignorance. Hence I always recommend, unless you are severely deficient, don't take supplements, eat the fruit or vegetable or meat or nuts or dairy or cereal or lentil. You don't know what you might be missing out.
So, would you be willing to take 20,000 IU of oral vitamin D, given what we know about the vitamin?
Let me summarize what I understood from your post:
1- If these sets of knowledge are "next to nothing", so we will never be able to know anything in... never.
2- If you are aware of these facts, you should know by now that natural evolution process works on try-and-error, rather than aimed constructions.
3- All these what you call "lack of knowledge" sounds like we know all ingredients but we do not know how do they work. It's like knowing all type of climate conditions, but not being able to guess what the weather exactly will be in a week or a month time. Here comes the computer capability, here comes the indoor environment where you can control the temparature and the armour of the building no matter what happens outside. So you will "construct" the artificial components depending on your project (let's say "healty survival of human bodies") using natural material (let's say everything you can obtain from nature).
And this is my comment: "Any suggestion that we can artificially tailor it to our needs is an argument from ignorance", but at the same time a challenge. We challenged nature before, send artificial satellites to outer space, even without knowing what gravity actually is.
You are telling me that it is utterly nonsense attempt to model our biologic system and food process, or it is totally impossible to play with DNA to create vegetable species which do not exist in nature. So, we will get nowhere or learn nothing (or "next to nothing") even if we started and followed such a project.
10 000 years ago our ancestors created an agricultural revolution and isolated some specimens (simply everything in your examples; fruit or vegetable or meat or nuts or dairy or cereal or lentil) without knowing anything about vitamins whatsoever. Yet you can recommend these artificially selected and altered products to other people.
I say this: Now is the time to use our knowledge. It is time to make serious experiments as our ancestors did in their time, and now we eat the "fruit". How can you know what you do not know if you do not try?