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.