Offset in exported mosaics and markers

[Duncan Bourne]

After many months I'm still working on orthomosaicking  historical aerial images and still battling unacceptable accuracy in my outputs. The inaccuracy is inconsistent between projects and in different areas of single projects and I'm at my wits' end trying to determine its source.
I'm determining my markers' coordinates based on our basemap and inputting those to Metashape, then exporting the marker file and comparing it to the same basemap.
The shift is identical in the exported mosaic and its corresponding exported markers, and the markers' numerical coordinates have been changed in the export process.
I've been speaking to folks at Agisoft who are helpful but they need to see a whole project and my projects are typically 300GB. I've tried making small partial projects but the errors seem to scale with project size and are thus barely visible in the smaller projects.
Attached please see three sets of coordinates; the originals in Metashape, the exported markers opened in QGIS and the same exported markers opened in ArcGIS Pro.
Can anyone help me figure out where this error is coming from? As the error is the same for markers and mosaic I think if I can pin down its origin for the markers it will translate to a solution for the mosaics.
Yours in frustration,
Duncan

[Paulo]

Hello,

I think the difference in coordinates is due to the fact the original MS coordinates are the source while the exported markers' coordinates are the estimated...

[Duncan Bourne]

Thanks for the reply Paulo.
So the points I enter for the markers are known correct points, and they're being moved, along with the mosaic, to an incorrect location.
What I'm aiming for is to correctly locate my mosaic by using the known correct locations, not have metashape move my points to an incorrect location and align the mosaic with that.
I'm afraid I fail to see what possible use there is for this process. These are known points, I'm telling Metashape "This point in the mosaic is definitely at this location" and Metashape then moves it somewhere else.
Am I using the wrong tool for this job? I can't really imagine that wanting my mosaic to align with the source of my marker locations is such an unreasonable or unusual request. Does anyone else's mosaic align with their known marker locations?
I really feel I'm misunderstanding some fundamental aspect of the task at hand and just don't know where to turn for help. I thought this was a pretty basic use of Metashape, especially looking at the complex and intricate uses I see elsewhere, yet this fundamental task of producing a mosaic that aligns with its marker points seems difficult if not impossible.
Do you know of anyone who can help me here?
Cheers, Duncan