Hi David,
This is similar to this post: Geoid 12B
I copy here the most important information:
Currently Pix4Dmapper can do some altitude conversions for known geoids (egm84, egm96, egm2008)
For other geoids, we can only apply 1 constant difference (Geoid Height Above a known ellispoid): https://support.pix4d.com/hc/en-us/articles/202558239-Select-Image-GCP-Output-Coordinate-System-#label12
(You need to know the difference between the NAV88 and a known ellipsoid - the one related to your horizontal coordinate system)
If the geoid varies a lot (not a constant difference), then the only solution is to have GCPs with the desired altitudes (in your case NAV88 altitudes).
So, indeed, if you add your GCPs with NAV88 altitudes, you can set the altitude as Arbitrary:
the software will give you the results in NAV88 (interpolating). This does not work perfectly (as the curvature and scale issues will not be taken into account) but it is a good approximation (especially for small areas).
In the future, we want to offer more options to our users: The user should be able to import a grid geoid file into Pix4Dmapper that will define the geoid altitudes for his/her area. This is something that our Product Development team will consider for future version of the software.
Hope it helps 