Most supermarket fruits and veggies that are genetically altered are done so for their shelf-life, or their retention of texture/flavors after having been frozen. As a specific example, there is a specific breed of carrots that grow that are EXTREMELY large, dense, and hard, that are used for canned soups, so they don't disintegrate after brining for many years.
Another thing about supermarket produce is the waste when, how you mentioned, the produce that doesn't look "perfect". People are very conditioned to a certain symmetrical shape to be aesthetically appetizing. Very few fruits and vegetables are consumed in their unprocessed form at home, so by the time you're drinking your smoothie you will never know your apple was oblong, but people have a problem with choosing to purchase those items with their money.
Another thing about supermarket produce is the waste when, how you mentioned, the produce that doesn't look "perfect". People are very conditioned to a certain symmetrical shape to be aesthetically appetizing. Very few fruits and vegetables are consumed in their unprocessed form at home, so by the time you're drinking your smoothie you will never know your apple was oblong, but people have a problem with choosing to purchase those items with their money.