Fruits have larger plant cells because of water. The application of more irrigation water can increase the size of some fruits and vegetables, and there is more money per pound gained with water-laden foods. Most organic producers apply less irrigation. Some conventionally grown crops are sprayed with chemicals that increase water uptake in cells, most notably grapes. These sprays are expensive, so it is not done on things like grain crops.
Fruits are bigger by breeding.
A. Hybrid varieties are often much larger in size than open-pollenated varities of fruits, vegetables, and grains. Not all food plants can be made into hybrids, but many are. There is no genetic engineering in making hybrid crops, but it involves some very elaborate plant crossing techniques. Again, they make a lot of money selling water-pumped foods. Organic growers need to select plants based on their ability to fit within an organic rotation program, that look good and taste good at the market, and that make them unique from what you get from a chain store.