I think you're getting it all confused. Chemical is different. This is where they use pesticides to kill pest, parasites and fungi on the plants. This keep the plant disease free. Most of these chemicals they use are obviously bad for human consumption.
Genetic Modification on the other hand is an entirely different process. Rather than using chemicals to treat something, they start with the genetic makeup of the plant. Our genome or that of plant's is like a cassette tape. It has alot of information on it, like the cassette it has a lot of songs on it. The geneticist is like a DJ, he decides what song he wants played and how long the song will play for. He can also decide he wants to omit certain words from the song. He can snip certain genes in plants genome, omit some and even add some if he likes. For instance, those of seedless watermelons and seedless grapes. He intentionally removed those genes so the plant do not produce seeds in their fruits. Some plants might have a genetic advantage to certain diseases and rather than grow a few generations of those plants to have better disease resistant plants, he can insert that gene to a disadvantage plant.
I have done a brief search on the disadvantages of genetically modified plants and have not come up with anything major. The exception is having proteins produced in the plants that might create allergies.
Genetic technology has made our life less difficult and there is denying about that.