We already see this with Cavendish bananas and the TR4 virus. We're doomed when something similar appears for common food like rice, wheat or livestock.
Engineering will favour whatever you want it to (Diversity, tastiness, colour, shape.). It's natural selection that will apply only one selection criterium: Most surviving offsprings.
How do you think we got this diversity in grain and vegetables?
For example rutabaga, turnips, kohlrabi, cabbage, collard greens, cauliflower, broccoli, Brussels sprouts, cabbage, mustard seeds, and rapeseeds were all created though engineering from the mustard plant.
Same goes for all grain that you eat today, they were engineered from a few shitty grass species.
As for tomatoes, good luck finding a non engineered one that isn't poisonous. Same goes for almonds.
Have you seen undomesticated banana btw? Go buy some Musa balbisiana. I hope you like large pits and bitterness.
Or dogs? How much diversity have you seen in wolves? How many crazy fucking dog breeds are there?
Engineering =!= monoculture. We all agree that monoculture is shit.
But going full hippy "let's only eat what mother nature provides" is as far removed from reality as possible. Mother nature provides bitter poisonous shit, that is full of seeds, so that you don't eat it and so that it can reproduce. It is up to man to take that and make it so that survival of the fittest means survival of the tastiest.
Secondly, even though I am very much in favour of a social state, so I am not arguing for capitalism in general here, capitalism is pretty much a unregulated market economy.
How would you describe most societies of the last few hundred thousand years?
Socialism and everything related to it is a very modern concept. That was only made possible through the abundance of modern industrialisation.
If anything, the communist states that claimed to be defenders of socialism (I wouldn't call them socialist in any way but, meh), have shown that they were the biggest proponents of monoculture.
How do you feed a billion people through state organised agriculture? Through fields that are hundreds of miles long, so that they can be harvested easily and efficiently by a single machine.
You can still see the industrial agriculture wastelands of this philosophy in east germany today. Wind that would normally be broken by vegetation and the borders of smaller fields can erode the top soil and leaves nothing but unusable desert.
Perhaps you mean that people don't want much variety and the market responds to this? Better engineering is also the answer there: the more we improve the process and reduce the costs, the easier it becomes for people to service niche markets with more obscure products. Again you can look to the software engineering world for parallels.
In a world of well-engineered food, your personal "farm" is a box in the corner, which you put seed in once a week and it spits out finished produce. The coffee machine of the farming world, if you like.
And its not like science can't produce /new/ varieties either, STEM isn't that much of a monoculture!