Hello Bruno,
The RMS error of the GCPs corresponds to the difference between the initial and computed positions of the GCPs. It is a local indicator of how well Pix4Dmapper fitted the model to the GCPs.
These geolocation errors do not assess the accuracy of the computed 3D points, i.e. the automatic tie points that make the model. They assess the consistency between the geolocation measured on the field and the geolocation as estimated by Pix4Dmapper when processing the model.
On one hand, our software tries to adjust the reconstruction using the GCPs meaning that the goal is to minimize the RMS error. This is why you ended up with 3 mm. On the other hand, the global absolute accuracy of the outputs should be closed to 1-2 pixels (GSD) horizontally (XY coordinates) and 2-3 pixels (GSD) vertically (Z coordinate) using GCPs. In your case the error wouldn’t exceed 10-15 cm.
More information on GCPs RMS error: https://support.pix4d.com/hc/en-us/articles/203604125
About accuracy of the outputs (absolute vs. relative): https://support.pix4d.com/hc/en-us/articles/202558889
Best regards,