Hello
RealityCapture does not support geoid model, and elevations which are connected to it. To avoid this issue I would recommend converting your heights into a system which uses ellipsoidal model. In your case it could be a good ide also to use GPCs in a wanted coordinate system.
You can try to add the coordinate system’s definition to the EPSG.XML file, which can be find here: C:\Program Files\Capturing Reality\RealityCapture
Also, for some geoids it is possible to use the workflow from this post: How to improve a registration - #11 by OndrejTrhan