According the latest news on our side that refer to the firmware v.1.7.0.90 and v1.7.0060 for the Inspire I and Phantom 3 Pro respectively, DJI now measures the absolute elevation above sea level using EGM 96 as the reference. They used to record the elevation above ground level but this is no longer the case.
However the vertical coordinate is still not fully reliable. Indeed, we made testing in our office here and we found that the vertical coordinate is off by several meters that can reach an error of 100 meters. Some users noticed the same. Therefore our developers suspect something wrong in the DJI EXIF regarding the vertical coordinates.
Note that DJI just released on April 7th new drone firmware, v1.8.1.00 and v1.8.80 for the Inspire I and Phantom 3 Pro respectively, that could fix the vertical coordinate issue. So far we do not have any feedback.
Nevertheless, the wrong elevation written in the EXIF does not affect the GSD. The GSD of the model will still derive from the real altitude when you flew the mission. At 100 meters, it will be approximately 4.45 cm/pixel with 12 MP images.
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