To answer your question, let’s start with the explanation of GMO food and then address the issue of using heat from a microwave oven.
GMO, which stands for genetically modified organism, is a technically incorrect term. Unfortunately this term has become the most recognized one used to describe crops that have been modified genetically to resist pests or withstand applications of herbicides. Plant breeders have been using selective breeding methods to develop plants that are stronger or have various color or taste characteristics for decades. Think of a tangelo or broccolini. They are both well-known hybrids that have used traits from each original species to create a new one. A tangelo is a cross between a tangerine and pomelo. Broccolini is a cross between broccoli and kai-lan. When breeders create these new fruits and/or vegetables they are crossing hundreds of genes in each plant to get the outcome they want.
With respect to genetic engineering, scientists are building on the knowledge of plant breeding by identifying just one gene that expresses a desired trait; subsequently inserting that gene into the seed of the plant being modified. This is a more precise way of developing new plant varieties and is in some cases even safer than traditional breeding. The food that is harvested from these plants or crops is essentially the same as the original plant or crop but with one different gene. The crops look the same, taste the same and have the same nutritional value as the original plant or crop. There are no live organisms in the new food, hence the reason that the term GMO is technically incorrect.
So the answer to the second part of your question is fairly obvious. Since the genetically modified food is the same in every way as the unmodified food, using a microwave to heat the modified food would be no different either. You correctly state that GMO corn produces GMO corn syrup which is found in many packaged foods and as previously stated the modified corn syrup is no different than the non-modified corn syrup. Both will produce the same results when heated in a microwave.