Lots of genes only seem to do one thing. HERC2 seems to only affect eye color. If you're asking if it's possible that maybe we don't have a 100% perfect understanding of genetics, then of course it's possible. It's always possible there's something we don't know. Science does not deal in perfect certainties.
Would I be correct is following your logic to the implication that there's a significant possibility for effects we didn't anticipate and don't understand in genetic engineering? Of course that's possible. That's why GMOs are tested.
Is it possible that there's some obscure, subtle side-effect we won't notice for a long time to come? Yes. Is it likely? As near as we can tell, no. Can this doubt ever be fully assuaged by science? Not reasonably on anything more complex than the simplest of yeasts.
Is this a special threat, uniquely applicable only to GMOs? No. The same potential is present - even greater, due to number of mutations - in selective breeding.
How do you counter the very obvious profit motive here? "Gee Beta Carotene I Understand That's Good For Your Health, I'll Pay A Premium For That". How do you prevent that profit motive from minimizing unprofitable research into long-term health impacts? Face it, there will NEVER be a money motive to really figure this stuff out, that's why we're only finding out about BPAs now: there's just zero money in doing anything but the minimum due-diligence, as forced on you by the FDA, which is already bought out anyway!
It's like the nuke argument. Sure GMOs are potentially fantastic but as a race, or at least this capitalist version of a race, humans seem to be incapable of managing technology this fearsome.
Are you saying there are genetic modifications that do _absolutely nothing_ but add vitamins to food? I not an expert, but that's not my understanding of how DNA works.