Thank you for uploading the files.
After processing the dataset I also get the offset in all three directions.
When it comes to the vertical offset (Z) it is most probably caused by the fact that the GCPs are measured in the respect to Geoid12B that is not directly implemented in Pix4D. More in the FAQ of the [Desktop] Processing DJI Phantom 4 RTK datasets with Pix4D community post.
Do you by any chance have the GCPs also in the WGS84 coordinate system (latitude, longitude)? I would like to check if the same offset appears when using the coordinates that are not yet transformed into a projected coordinate system.