In order to get the best accuracy in the coordinate system transformations, our recommendation is to get the .prj file from epsg.io and ensure that it contains the most precise TOWGS84 parameters.
For example, let's say that the GCPs are given in DHDN / 3-degree Gauss-kruger zone 4. What .prj file should be imported?
1. Go to epsg.io and search for that coordinate system.
2. This particular coordinate system has four available transformations.
3. Select the most precise one which covers the area you are working on (in this case, accuracy 1.0 m, code 15949 [grid] )
4. Scroll down to the export section on that website, select Well Known Text as HTML and click Download.
5. The downloaded file can be used for the GCP definition on Pix4Dcloud Advanced or in Pix4Dmapper before uploading the project files.