(I know this is about Rifftrax, but we don't have a Rifftrax community.)
Genetically modified plants is very different from selective breeding. Selective breeding mimics the natural evolution process, removing natural selection and replacing it with human decisions.
Using a separate root stock from your fruiting trees isn't genetic modification or breeding. It's just taking desirable size features from a root stock and growing your desired fruit from that. It still remains two different plant, with two different DNAs. The fruit would produce a child of the fruit tree, the same as if it was grown from seed. If the root tree was allowed to flower it would create a seed the same as if it were never grafted.
GMO are an extremely useful technology. When well regulated and tested will help produce food for the growing world population. The big problems with it are the consequences of it. Plant have been modified to tolerate high doses of weed killer, pesticides and fertilisers. These all help increase the productivity of the land, but the impacts are terrible on the local environment. Residual weed killer and pesticide may pose a risk to human as well.