4. Farmer now saves/replants GM seeds he grew out of contract.
Well... This will screw a farmer over in the long run. Without the hybridization breeding schemes employed by Monsanto, Syngenta and other agro companies who carefully controll the genetic constitution of their seed lines, a farmer doing this will inevitably develop inbreeding depression in their crops and suffer some nasty crop failures.
4.a "Farmer learns to outcross crops, or hires a PhD plant breeder," and maybe this scenario would be more plausible. Absent a controlled breeding scheme, serious problems will arise. This is what farmers are paying for and signing contracts for - not solely the presence of a resistance gene in a given crop. Controlled breeding that ensures plant vigor is far more important in the long run.
Just a nit-picking detail, but it might be important to remember when considering the bigger issues presented in the article.