I have GCPs from an EMLID receiver based on WGS84 ellipsoid. I used the UNAVCO tool to convert them to orthometric, but also recorded the EGM96 geoid values at each GCP. Does everyone typically use the orthometric to help measure volume or measure plant heights? Is there any point to just using the geoid value, which is pretty similar across the small area?
First of all, I would say that orthometric heights are synonymous with geoid heights.
The choice of a vertical coordinate system depends on the coordinate system in which you would like to obtain your outputs. There are many vertical datums out there, it all has to do with your personal preference or if you plan to overlap the outputs with other data layers. EGM96 is a global geoid model, so it is expected to not approximate the region very precisely. Local geoids are of course ideal. More information can be found here: How to define Pix4D outputs with respect to a Geoid model.