Hello,
Please have a look at the following community post (Processing DJI Phantom 4 RTK datasets with Pix4D) which will give you some recommendations on how to process that type of data.
I am not sure about your question but the Phantom 4 RTK will capture the geotags with respect to WGS84, which means ellipsoidal height. If you use those altitudes directly, the point cloud and all of the products that you can get will be referred with respect to the WGS84 ellipsoid.
If you want to get your outputs with respect to a geoid model, please read this article here.
Regards.