I have the same question- I'm trying to load GCP with the vertical datum as NAVD88, but the dropdown when importing GCP's into Drone2Map does not have the option to select NAVD88. Options I see are EGM 84, EGM 96, EGM 2008, No Conv, or Const shift without any descriptions on what they are.
In Australia because D2M doesn't support the Australian Geoid, we set the Vertical coordinate system to Const. Shift. We then edit the Geoid Height to be 41.03716.
Perhaps you can do something similar if you know the Geoid Height for NAVD88?
Assuming that the xy coordinate system datum is NAD83 and z uses vertical datum of NAVD88, you could use this tool to determine the Geoid12B height above the NAD83 ellipsoid. GEOID12B GEOID HEIGHT COMPUTATION
Just enter a point near your GCPs to get a Geoid Height.
Then when you are importing your GCPs into Drone2Map choose Const Shift and enter the Geoid Height.