According the latest news on our side that refer to the firmware v.188.8.131.52 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.
As a consequence, we always recommend to process with ground control points (GCPs) in order to fix these uncertainties.
About using GCPs: https://support.pix4d.com/hc/en-us/articles/202558699
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.