"The difference is the methods involved, where people artificially interfere with breeding and natural selection by means of selecting crops themselves or directly cut and paste genes to that effect."
And that's the whole point. You want to be logical, OK. Let's be logical and scientific about it:
History has shown me time and again that giant multinational corporations are more concerned with doing things the PROFITABLE way, which is not necessarily, the safest/smartest/cleanest/healthiest way. So WHY should I believe that ADM, etc. won't do something "bad" to my food, cover it up, and lie about it?
It's not about being a luddite, it's about knowing, from experience, that the CEO of the company in charge of "Engineering the Future of Our Food!" is probably an asshole who doesn't care what impact he has on other people or the environment.
Additionally, I don't know about you, but I gave up on the notion of the "noble researcher/scientist a long time ago. From his (scientist) perspective, his job with the big food multi-national is probably just as soul-crushing as any other corporate gig.
"Should I check those test results one more time? Fuck it! It's Tuesday, my boss is an ahole, I've got to fill out my 10 page quarterly review, and I just don't fucking care right now. I'm going to Chotchkie's..."
Yeah, I want those guys tinkering around with the basic building blocks of my food.
TLDR: You assume there's no reason to NOT trust them, and I say there's no reason TO trust them.