When using both camera priors in the WGS84 coordinate system (GPS) from images as well as ground control points (GCPs) in a different coordinate system at the same time, you need to make sure that you use the same vertical coordinate system.
If you wish to geo-reference your scene only with ground control points, you need to disable camera priors from your images (via ALIGNMENT tab – Settings – Camera priors – Enable set to False) and align the images with the placed GCPs. In this case your project will be geo-referenced only using coordinates from GCPs.
When using both camera priors and GCPs, RealityCapture considers both sets of coordinates. In most cases, GPS coordinates from camera priors are less precise that coordinates of the GCPs, and using both sets can lead to larger errors.
You can also define the weight for both sets of coordinates. By default, camera priors have weight 1, 1, 0.8 for X, Y, Z coordinates respectively, and GCPs have weight 10 for each X, Y, Z coordinate.