Hi @mja and @andrew.parsons ,
As @Jason_Hagon mentions, PIX4Dmapper does not support grid transformations, which are those required to accurately transform your project’s Image Geolocation Coordinate System (WGS84) to your project’s Output Coordinate System before processing your project. When RTK geotags are used, this type of transformation is needed to preserve the RTK accuracy. PIX4Dmapper also does not directly support geoids.
Therefore the workaround is to convert your horizontal and vertical image geotags in third-party software before importing them for processing, define the output horizontal coordinate system as needed and the output vertical coordinate system as arbitrary.
More information about the topic can be found at these links:
Horizontal grid corrections and transformations
How to define Pix4D outputs with respect to a geoid model
Select Image / GCP / Output coordinate system
PIX4Dmatic does instead support grid transformations and local geoids.