When I read that, it was kind of alarming to me. But as you said, should be easily fixed if true.I don't process in Drone Deploy or Pix4D. But in Metashape, you have options that should, in theory, result in the same output. If the drone uses WGS84 exclusively, that makes sense and is a good thing. @elistechnology mentioned he thought that the WGS84 elipsoid model on the drone may be off, which is not good but if true could probably be fixed easily with FW.
I am still unclear on the whole Evo 2 RTK workflow.
What is your NTRIP using? WGS84 or NAD83(2011)? I assume that if Evo 2 RTK outputs in WGS84, doesn't it need the input corrections to be WGS 84?
Are the elevations in your images and control points ellipsoid or orthometric heights?
Off topic, but can you use an Emlid RS2 as a base station set on a known point and send corrections to the Evo 2 RTK using the LoRa radio?