How novel are the genes introduced during genetic engineering?

It is often asserted that genetic engineering (or GMOs) are different and should be regulated differently because they introduce "new" genes that couldn't have been introduced "naturally."

A piece at the genetic literacy project by Curtis Hannah, a plant geneticist, however, questions that wisdom: 

The remarkable advances in the way DNA is sequenced have made the sequencing of all the genes in a particular organism (termed the genome) extremely cheap. Thousands of genomes from different organisms have been decrypted and comparative genomics is a thriving field of scientific endeavor. Investigators have also sequenced different members of a particular family and unexpectedly found that the two different members of the family did NOT contain the same genes. Some genes were found in some members of the family but not in others. This phenomenon of plus/minus genes is particularly rampant in plants.

An exceptionally striking case of this was published recently in the journal Plant Cell. Of 8681 corn genes studied at the DNA level by this group, only a small fraction, 16.4 percent, were found in all 503 lines examined. The vast majority of these genes (83.6 percent) were found in some BUT NOT ALL lines. Corn is not an exception since similar cases of plus/minus genes have been found with other important food crops. Hence, new non-GMO or conventional varieties of food crops appearing on the market this year likely contain genes that were not in those same crops the year before. Also, the new ones likely lack genes that were present the year before.

Where do these genes come from? There are several sources. First, most food plants underwent a duplication of most if not all their genomes during their course of evolution. This duplication then allowed some relaxation from Darwinian selection such that the one gene copy was free to diverge in sequence and take on a new function.

He concludes:

To summarize, the new methods to rapidly, accurately and cheaply decipher genomes have uncovered hitherto unimaginable variation in the genetic material of all organisms, including the ones we eat. Hence, labelling plants and their derived foods GMO and non-GMO is clearly a distinction without a difference.