Hello,
I would start with the Dewarp that was mentioned. We do not recommend de-warping images (fixing the lens distortion) before using them in RealityCapture. We have our own lens distortion algorithm and therefore de-warping them twice can cause issues.
If you don’t want to use the lens distortion model in RealityCapture, make sure that all Prior lens distortion settings are set like this (CTRL+A to select all inputs):
Are your inputs in the same coordinate systems? I assume you are using a combination of laser scans and images.
You are mentioning a reference point. Are you using a manually created point in RC? Is it a ground control or ground test point?
The 40cm deviation on the Z axis could be related to the elevation system. The WGS84 system is a horizontal system and does not define heights. Are your heights related to ellipsoid or geoid?