I also use Pix4d but had not yet learned of the editing feature of the GCP manager. Would have saved me some $$. But I got the job done that triggered the post, and since then have done another mapping job, also with Pix4d and now using ArcGIS Mapper to overlay as-built orthomosaic and contours on the architect's plan. Kinda cool.
Regarding the altitude to be used in mapping engine, that entry needs to include the difference between the geoid and the ellipsoid heights at that location anyway. So it's not going to happen that any of the EXIF altitudes in the photos can be used as-is anyway. LIke AxelZ, I also shoot a rover fix at the takeoff point and use that for later finding the altitude to be entered in the GCP table.
Having the right altitude makes Pix4d a lot more accurate at grouping the photos to be marked as GCP's. i guess I was just not expecting the EXIF absolute altitude entry in the
P4P's meta data to be an absolute fiction. The baro relative altitude is useful, but otherwise the altitudes are useless. Maybe the
P4P RTK edition has this sorted out, but I have no knowledge of that bird.