There is a difference between GMO and hybrid seeds.
Genetically modified means the seeds have been altered in a lab with other products. From Appendix A of the Standards mentioned in their email -
An organism in which the genetic material has been changed through biotechnology in a way that does not occur naturally by multiplication and/or natural recombination ; cloned animals are included within this definition
Hybridization has been going ever since people began cultivating crops. (My grandfather showed me how he made hybrid roses for my grandmother.) This process involves combining separate strains through cross pollination, and the point was to create a new strain that would do better in a specific place with certain soils. This process took several years to complete, and seeds could be used for next year's crop.
Thanks to the work of Mendal, (I still recall studying this in school so long ago) big companies got into agribusiness because they could produce hybrid seeds in one generation, but the catch is that the seeds of these plants do not have the same characteristics as the parent crop. This means that farmers have to purchase new seeds each year, AND these crops often require special fertilizer and pesticides.
After reading through the material on the Non-GMO Project site, I don't doubt their sincerity or methods. If you want a real kick in the head read pages 28 and 29 of the Standards cited in their email. It describes the high-risk crops and products, such as vitamin C additives and supplements.
This certification does not go far enough for me because fertilizer and pesticides are just as much as menace to healthy foods. It might be just me, but when I see the little non-GMO label, I think the food is safe. I wonder how others view this label? So, the certification is valid, but I want better food, which means certified organic.
However, I can see a bit of a pale silver cloud lining. With more public awareness, people are seeking non-GMO food, and more and more food providers are listening to their customers. Of course, I doubt the public understands that the crops were likely dosed with chemical fertilizers and pesticides. Also, for some crops such as corn and soy, recovery to large harvests with non-GMO status could take years because so much contamination has occurred.
Some of this info comes from an article on Food Renegade
http://www.foodrenegade.com/hybrid-seeds-vs-gmos/