Phantom 4 Pro doesn’t record the drones true GPS altitude properly. It is heavily weighted toward the barometer’s elevation values. I’ve seen it differ greatly when flying the same site a week apart when the barometric pressure had changed.
This doesn’t cause me any real issues now that I know what’s going on. I can choose to export the image location values from pix4d to a .csv file and adjust the altitudes to what they should be, and reimport the image locations into pix4d.
If you have GCPs like Julie mentioned above, you can let pix4d adjust the data to the GCPs. I normally just pick 3 GCPs and mark them in the basic editor and reoptimze. This will shift the data into the right location. I then mark any remaining GCP and checkpoints in the raycloud editor and reoptimize once more and regenerate my quality report.
RMS values should be good if your GCP locations are accurately marked. I typically see RMS values of .02’ - .04’ when using centimeter grade located GCPs. The elevation inaccuracy should not affect your RMS values. Your RMS value indicates an inaccurately marked GCP or non survey grade accuracy of your GCP points.