It's inferior because we aren't adapted to it. Our bodies are highly adapted for millions of years to thrive on the food that comes out of our biosphere more or less directly. This is why super-hybridized dwarf wheat (not even GMO!), for example, which was developed in the 1960s, has been linked to all kinds health problems, including obesity. Our bodies have not had time to adapt to it, but if we look at dwarf wheat purely through the lens of economics, it's a "great" product as it has twice the calories of ordinary einkorn wheat that we've been eating for more than 10,000 years.
Would you care to address the specific question posed? Like, why Golden Rice is inferior to the rice varietal from which it is derived? Just because it doesn't come with a "100% Natural!" stamp doesn't make it bad. Neither, I should think, is the converse true. As you illustrate, there are plenty of problems with "natural" non-GMO plant breeding.
Is the position that you mean to stake out perhaps that it's possible for GMOs to be inferior, rather than that they are necessarily so?
I know nothing about Golden Rice so I can't comment on that. I think the position I'm making is that it's likely that GMOs will be inferior for all the reasons already cited. If you're trying to be more profitable, you put nutrition in the back seat. If food is just a bunch of macrobiotic chemicals disregarding a looong history of natural selection with intricacies we've only begun to understand, chances are you will not "get it right" in terms of nutrition and health of the consuming organism.
