I love your questions because it allows me to address some of the confusion out there concerning GMOs.
The ability to precisely insert a gene at a particular site in the genome is an area of active research. The day likely will come when all new gene inserts are done at precise locations. However to the best of my knowledge all commercially used gene inserts in today’s market arose from methodologies that did not use precise insertion techniques. However, following insertion the location of the inserts in commerce was precisely determined by DNA sequencing. Knowing this information then allows one to determine whether the function of any endogenous gene was abolished by the insertion.
How a gene functions in a plant – regardless of whether it is foreign or endogenous – is another area of active research. There are about 40,000 genes in a typical plant and how each of these genes precisely functions is known for only a tiny fraction. On top of this, it is now known that not all endogenous genes are present in every line of a particular plant. In corn for example, there are about 400 genes (1% of the total) that are not present in two inbreds lines chosen basically at random. Hence, “new” genes are inserted in today’s new hybrids simply by conventional breeding. The bottom line is we know much more about how newly inserted genes function in a plant than we do about the genes that were already there.
You are correct in saying that genes work in families. The whole area of “biochemical genetics” is based on the fact that different genes encode enzymes that work in a pathway (much like an assembly line) to make a particular compound, be it starch, protein, lipids, vitamins, pigment, etc. In addition, it is now clear that there is usually more than one copy of a gene in the genome. Some of this is for tissue specificity (some genes are expressed only in the seed, some in the leaves, etc.) so this area is quite complex. The discovery of genes functioning in pathways and that there are multiple copies of a gene, however, is old information. The Nobel Prize for the discovery that genes encode enzymes was awarded around 1956.
Your discussion of equivalency raises some interesting points. What is tested for “equivalence” is the feeding value of the produced crop and other issues like the absence of new allogeneic proteins or other adverse chemicals. If the newly inserted gene is expressed only in the leaf and nothing produced from the new gene in the leaf flows to the seed and you eat only the seed, then by definition it is equivalent.
You should also note that plant patenting was done long before gene technology was invented. Some inbreds are covered under utility patents while most plants are protected by the Plant Variety Protection Act. I say this because there seems to be the idea out there that companies had no way of protecting their elite germplasm and finished hybrids and cultivars before biotechnology came about.
I hope this answers your questions.