Before I give my answer let me provide some background so we are all on the same page.
Organic produce is edible food stuff from plants grown without the use of use of synthetic fertilizers or pesticides on the plants or in the soil. A GMO is a genetically modified organism. Once this term used to mean any sort of breeding but with the rise of DNA technology where genes can be inserted into an organism, GMO has become more focused and applied to organisms where a gene is inserted. The plant has been engineered (someone thought of what was there and added something).
One type of engineering people are familiar with is GM Soy or Corn where the adult plant can withstand herbicides. So, by growing GM Soy the farmer can spray a herbicide safe in the knowledge that it wont kill his /her Soy but only the weeds that compete with his/her crop. This is true only until the weeds evolve resistance against the spray.
You can plant GM seeds and they will have not pesticide or herbicide inside the seed. They may have coatings of fungal or bacterial killing compounds but that is a treatment one can apply to any seed, GM or not.
When the GM seeds grow a grower might choose not to treat them with synthetic fertilizers or pesticides and t think they are growing organically. However, even though you have not used synthetic chemicals you are not growing organically according to U.S. National Organic Program Regulations. I pasted the section at the bottom, from that document. GMOS are an 'excluded method'.
To answer the question. You cannot ask if the seeds are "inherently better about seeds that were grown organically". That is because lots of things in the genome of the plants are different since GM engineers would have selected a different race of plant to work with. The non-organic might have been traditionally selected (through breeding) to have desirable traits. Or the GM plant might have them anyway which had nothing to do with the engineering.
I think the decision must rest with what a grower would want to do with the produce. If you want to sell/gift/exchange it as organic you cannot use GM seeds. If you don't want to then the choice is really up to what grows best. A little bit like Heirloom tomatoes, you choose what you hear grows best and suits your needs. But the whole point of GM is that the seed contains instructions to respond to some later treatment (e.g. pesticides) so it would not make sense to buy them and not use that
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from U.S. National Organic Program Regulations
"Excluded methods. A variety of methods used to genetically modify organisms or influence their growth and development by means that are not possible under natural conditions or processes and are not considered compatible with organic production. Such methods include cell fusion, microencapsulation and macroencapsulation, and recombinant DNA technology (including gene deletion, gene doubling, introducing a foreign gene, and changing the positions of genes when achieved by recombinant DNA technology). Such methods do not include the use of traditional breeding, conjugation, fermentation, hybridization, in vitro fertilization, or tissue culture. "
http://www.ecfr.gov/cgi-bin/text-idx?...
