You're mistaking genetic modification for natural hybrids. The two are not the same. Splicing together genes from different organism in a lab (fish cells/tomato) is quite different from the natural result of cross pollination. The example you are using is flawed and a false talking point made to try and draw inaccurate examples between the two. One has its limitations in nature vs modifying that which could never naturally occur.
The formulation of a vitamin can result in one brand having a lesser quality when it comes to absorbtion than another. The point I am trying to make is that increasing the vitamin content may not necessarily make it more nutritional. The method that is used to increase the vitamin may not result in the same potency found in the natural version of the fruit/vegetable. This is due to the vitamin no longer being the same molecule as it has been modified. The fruit/vitamin would no longer have the same molecular structure.
You're showing that you know very little about genetic modification. The term is very self-explanatory. You modify the genome of a plant or animal. How do you do that? You can do it in the lab through various means such as gene knockouts to remove deleterious traits or horizontal transmission to add beneficial traits such as drought resistance. When you add a gene, the RNA polymerase transcribes that gene and the ribosomes translate the protein that grants the plant or animal that beneficial trait.
You can also do it by crossing two individuals in which each parent has a specific advantageous trait. Let's say these traits are dominant and are on different loci. Sweet fruit is on loci A and large fruit is on loci B. Parent #1 has sweet, but small fruit and is homozygous dominant for the sweetness, so its genotype is AA bb. Parent #2 has large, but bitter fruit and is homozygous for large fruit, so its genotype is aa BB. You cross these individuals together and their progeny will all be Aa Bb. Because both loci have dominant alleles, the offspring have both sweet and large fruit.
Your last paragraph also shows how little you understand chemistry. Nomenclature of chemical compounds is determined by what strucutural types (e.g. double C=C bonds, rings, disulfide bridge, etc) and orientation (e.g. trans, cis, L-, R-, etc) they have. If a "vitamin" is an entirely different molecule, then it is no longer a vitamin. A "lower quality" vitamin supplement is lower quality not because of the vitamins. It's lower quality because of the lower concentration or shoddy synthesis of the supplements.
I think you're being turned off by the fact that genetic modification is sometimes done in the lab. When you hear the word "lab", you're probably imagining a bunch of white coats in opaque safety goggles injecting mysterious blue liquid into a tomato. The negative connotation is what makes you against GMOs. But here's the fact: nearly everything we eat is genetically modified. If you want to eat "naturally", then good luck.