To clarify the situation when dealing with offset because of inaccurate vertical coordinates, there are two ways to adjust the model:
1. Using points with accurate vertical coordinates and including them into the project as GCPs.
1.1. Ideally these points are actual GCPs measured on the field with accurate GPS device.
More information about getting GCPs: https://support.pix4d.com/hc/en-us/articles/202557489
More information about including GCPs: https://support.pix4d.com/hc/en-us/articles/202560239
1.2. These points can also be obtained from a Web Map service but it will be less accurate.
More information on how to proceed: https://support.pix4d.com/hc/en-us/articles/115000778603#label2
NOTE: In somes cases because the vertical shift is too large, the software cannot match the points and the model so it is not possible to mark them in the rayCloud. This article will then probably help: https://support.pix4d.com/hc/en-us/articles/206544136
You can also check our video on the same topic: https://www.youtube.com/watch?v=539e7la_zzo
INFO: Once adjusted, if you want the model to be visually pleasing in the rayCloud, e.g. without long rays linking the blue (wrong / initial) and green (corrected / computed) camera spheres, it is possible to edit the image vertical coordinates and to re-optimize the results so that they will be displayed closer to the accurate position. For more information: https://support.pix4d.com/hc/en-us/articles/115000778603#label1
2. Editing the image vertical coordinates. It is a good option if the image vertical coordinate is constant during the data acquisition, e.g. grid horizontal flight. The true absolute altitude of the images is assumed to be known.
More information on how to proceed: https://support.pix4d.com/hc/en-us/articles/115000778603#label1
It is true that there are quite some cases where there is an offset between the image geolocation position and the generated model. The procedure on how to deal with this is also described in this video: https://www.youtube.com/watch?v=539e7la_zzo
Hope it clarifies the situation.