RickInRealLife, the best part about pleiotropic effects is that they are pleiotropic! If there was something inadvertent happening that was seriously affecting the physiology, development or metabolism of the plant – it would stick out like a sore, well, leaf.
The claims that there are some unintended glossed-over issues are great to generate an alarmist response, but don't hold much weight in reality. The idea is predicated on the possibility that gene inserted (the "transgene") may land in a place where it has some role in eliminating a resident gene's function or perhaps increasing it. That COULD happen. It DOES happen.... but is it something we need to worry about?
Certainly we need to know if something collateral happens. The first indicator might be that the plant itself would never develop or would have severe problems. Remember, they harbor the transgene and their cells share a lot of similarities with ours. If there was a problem, you'd see it.
Today our tools are extremely sensitive. If the insertion of the transgene had an effect on gene expression (a super sensitive process), we could figure it out in a few days using a process of RNAseq. Changes in proteins could be visualized with proteomics and metabolic techniques could show changes there. Basically, if there was a pleiotropic effect, or even a minor collateral one, science would find it!
Remember, these genes are engineered into elite backgrounds that are highly productive on their own. The big co's are going to be darn sure that the inserted gene will not compromise the genetic integrity of the plant, or its safety for those consuming it.
But just to give you something to think about... if Antoniou and others fear effects of a transgene, imagine how much sleep they'd lose if they learned about transposable elements. Transposable elements are natural "jumping" sequences found in massive numbers in many plant genomes. They move, reinsert, wreck, create, and remodel genes and genomes all the time. If you see a problem come up in a GM plant it is much more likely that a natural jumping gene did it long before the transgene did!
In the end it is an outdated argument. Today's tools are so sensitive that anything detracting from the safety or quality of the final product would be recognized and eliminated – in the unlikely event that it happened at all.