The huge difference is who holds the patent. The example you gave involves Monsanto, the patent holder for several GMO crops, and a terrible company that does everything in its power to make money by exploiting people. Golden Rice, however, is patented by the scientists who designed it, who likely only patented it so that a company like Monsanto couldn't just make some similar GMO and patent it instead, using it to exploit people even more.
This same thing happened back when genes themselves were able to be patented; some companies like Myriad Genetics would patent genes like the BRCA gene, a common source of inherited breast cancer predisposition, so that they could charge an arm and a leg for testing. So, researchers and non-profits would patent genes that they found just ensure they could be fairly studied and tested for.