Davis, I LOVES me some Scientific American. It always has been a pretty reasonable resource at the interface between science and an interested public. I read the article you cited, and it is raised all the time by critics of biotech. It is the one place in a reputable source where you'll find the claim that researchers cannot do research on Big Biotech's seeds. Note the use of "one”.
Being a fan of SciAm, I can't fathom what must have been in the water cooler that day. The work is authored by "The Editors" and they have been historically pretty good. My guess is that this was in the transition in 2009 when John Rennie was leaving and perhaps something a little flimsy snuck in.
I say flimsy for two reasons. First, any academic researcher can get the seeds, and second, anyone with a few hundred bucks can have transgenic plants made.
The Big Ag companies have Academic Research Licenses. You are free to use their stuff, you just can’t grow it and sell it (duh). There are no restrictions on publication and they don't care what you are up to. A student I know recently went on an (unsuccessful) allergen search in some GM soybeans. It was simple to perform independent research without restriction.
You also can go to any of the several universities around the country and pay to have transgenic corn, canola, tomato, and a dozen other crops made. It's reasonably cheap, like $600 per line. That's not too much for a researcher with a hunch that GM food has a major problem. A simple hypothesis with a few good controls might run a few grand, but that's peanuts compared to the Nobel Prize money if it turns out to be correct!
All of this is said understanding that there are significant restrictions on GM crops. In order to grow/use/handle the materials you have to be certified and play by USDA/APHIS rules, which means you have to have tight controls on insects, pests, pollen and must be able to destroy the materials. Regulations are really tough! That said, a phone call and a Fed Ex number and I could have materials in my hands in a few days.
In short, anyone claiming a conspiracy to squelch independent research just hasn't tried to do it. There are many avenues to get the seeds, and since they have the most to lose, I'm guessing the big companies are THRILLED to have independent researchers find a problem if it were to really exist.