"Tilling" - modifying plants using non-gmo? methods

Here's an article from Wired magazine on stressing plants by putting seed in various chemicals to produce mutations, then using the mutated genes to produce specifically wanted or beneficial traits. Can this be still considered frankenfood? In nature plants naturally produce many mutations. For an example there are more than 400 different varieties of japanese maples and more are added every year through natural mutation and with help from human growers pollenating flowers of different varieties. Tulips, roses, orchids are other examples. But somehow I'm uneasy when food is purposely manipulated. Of course humans through the ages have chosen the most productive and good tasting plants and animals to consume and breed but these were obtained through natural mutations. Doesn't sound like much of an argument against "tilling" but the unease won't go away.