You forgot one thing. The direct genetic manipulation, while giving desired results much faster compared to selection, is not stable or predictable.
Because, when using selection, the plant tests it itself - by surviving or not. Several plant generation loops and analysis, and done. This is not the case with direct manipulation.
It takes a LOT of resources to simulate the plant development and calculate the impact. It takes a lot of money and time to run test cases to stabilize the whole changes and iron out even tiny quirks.
Only then direct genetic manipulation is safe.
This is not being done. Instead money making is done - safety does not interest people, they are used to dump wastes without thinking of consequences, like babies peeing in own bed.
This is why genetically modified food possesses danger much beyond the scope of a nuclear meltdown.
Tschernobyl case, with tremendous efforts, was managed.
But you can't manage where genetic damage is driven, you can't control where the bee flies.
http://www.youtube.com/watch?v=nIJbA5BJFiQ