Help With CRS and Vertical Datums

I have a project with PPK tagged images in WGS84/Ellipsoidal height. I also have GCPs that were collected and processed through OPUS and compiled into a .csv with both ellipsoidal height as well as a column for orthometric height. My question is, can I use those GCPs and have the output data have the elevations in NAVD88, rather than in ellipsoidal? How do I need to set up the image CRS, the project CRS, and the GCP CRS in order to make this work? I work for the Government and we have to have the vertical values in orthometric height (NAVD88). I originally setup the image CRS from the defaults from the WingtraOne camera (WGS84 w/ellipsoid height over the WGS84 ellipsoid) and set the GCP CRS to WGS84 w/NAV88 us feet for the vertical along with Geoid 18 (shown on the OPUS results). The actual GCP .csv I uploaded was referencing the Elipsoid Height field…because it did not want to accept the .csv with the orthometric field used. I also set the display units at the bottom of Matic to US Survey Feet and after marking GCPs and re-optimizing, I yielded the below results. Can someone please help?!

Camera SONY_DSCRX1RM2_35.0_7952x5304
Average GSD 0.088 ftUS
Project CRS WGS 84 / UTM zone 15N + NAVD88 height (ftUS) - EPSG:32615+6360 [GEOID18]

Quality check
Matches Median of 12347 matches per calibrated image
Dataset 99.91% calibrated (24619/24641), 1 block
Camera optimization 0.16% relative difference between initial and optimized internal camera parameters

GCPs 21 GCPs, Mean RMS position error 0.395 ftUS / Sigma 0.390
The GCP position error is more than 2.5 times the average GSD.
Checkpoints 0 Checkpoints
MTPs 0 MTPs
aITPs 0 aITPs
mITPs 0 mITPs
ATPs 107692662 ATPs

How did you correct your images to WGS84/Ellipsoid?
If you used NGS CORS stations, they send data in NAD83(2011)/Ellipsoid. But you could easily transform this to ITRF2014/which equals a realization of WGS84.

On your GCPs, are you using the NAD83(2011) or ITRF2014 outputs that OPUS gives?

To answer your questions:

My question is, can I use those GCPs and have the output data have the elevations in NAVD88, rather than in ellipsoidal?

Yes, the GCPs will shift/transform the data.

How do I need to set up the image CRS, the project CRS, and the GCP CRS in order to make this work? I work for the Government and we have to have the vertical values in orthometric height (NAVD88).

First figure out if your PPK corrections were done in NAD83(2011) or ITRF2014. If you used NGS CORS, my guess is your image data is now in NAD83(2011)/ellipsoid.

Change your image system to NAD83(2011) ellipsoid if that is how you PPKed it from a CORS.

Using GCPs will place your project in that datum/system. Use the orthometric elevations in your control points and set the datum to the datum used to create them in OPUS. Change your vertical system to NAVD88 Geoid 18.

Since you have PPK corrected images use the accurate pipeline choice.

My only issue is that you are using NAVD88 with WGS84. NAVD88 is a local vertical datum tied to NAD83(2011). Since you are using a projected WGS coordinate system, this is technically not correct since WGS84’s current realization does not equal NAD83(2011). I would use a State Plane for my projected system.

In the future I would do this:
PPK your images to NAD83(2011) geographic with ellipsoid elevations.

Collect your control points in your desired output system. I would use the correct State Plane US Ft. Collect double the points so that you have both GCPs and Check Points. When you define your control points system use NAD83(2011), Your correct State Plane US Ft, Vertical system of NAVD88 USft and Geoid 18.
Use the accurate image pipeline option.