You yourself point out an important difference - plant patents cover a single variety, utility patents cover every variety with a particular gene, no matter how it got there. (And the ability to save seeds is not "irrelevant for hybrid crops" - yes, you lose most of the benefits of having a hybrid variety, but farmers do it anyway because for some plantings the cost saving is worth the loss in yield.)
What's more, there's also quite a nasty patent thicket covering the techniques used in creating GM crops, so you can't just dodge the problem by going out and creating your own GM plant. It's one of the reasons golden rice was doomed to fail - it requires patent licenses from something like 30 companies because of the techniques it uses, including all the big biotech corps. Its creator managed to get heavily restricted free licenses for them because it made a good PR weapon against anti-GMO activists (his explanation), but the conditions make it pretty much useless. Only subsistence farmers or countries which can't grow enough calories to feed their population are legally allowed to grow it, and out of the latter I think only the Philippines even has the right climate to grow rice.
What's more, there's also quite a nasty patent thicket covering the techniques used in creating GM crops, so you can't just dodge the problem by going out and creating your own GM plant. It's one of the reasons golden rice was doomed to fail - it requires patent licenses from something like 30 companies because of the techniques it uses, including all the big biotech corps. Its creator managed to get heavily restricted free licenses for them because it made a good PR weapon against anti-GMO activists (his explanation), but the conditions make it pretty much useless. Only subsistence farmers or countries which can't grow enough calories to feed their population are legally allowed to grow it, and out of the latter I think only the Philippines even has the right climate to grow rice.