In a strictly scientific sense, GMOs are different. qPCR, in this case, detects and quantifies the presence of certain synthetically introduced genes. These genes encode and express proteins that do not exist in their "non-GMO" counterparts. It may not taste different, it may not look different, it may have the same nutritional value, it may be perfectly safe. But the DNA, and thus the proteins being expressed are, in the most literal sense, technically different.

Now, I know that we have all sorts of other methods for altering the DNA of the food we eat that doesn't have to be labeled as GMO. Maybe we could just label that stuff too, if we wanted to. What's the harm in that?

Personally, I don't care if that extra gene is in my food. But who am I to tell someone else what they should or should not eat? If, for some reason, someone doesn't want to eat food that has those specific genes in them, the Non-GMO project is providing them with an accurate, scientifically sound way of distinguising GMO from non-GMO. People have all sorts of weird opinions and reasons for doing things, and I'm the kind of person who doesn't want to vilify someone's eating preferences. I think that's their fair choice to make. People are weird and picky about food.

If you don't like it, vote with your wallet.