Thank you for your response! I thought if I didn't check the markers in the reference pane, they would remain independent.
A couple of clarification questions:
1. When you say "clear location for reference point," do you mean right click the marker and clear? This removes XYZ and keeps the markers on the photos, but when I export the markers there are no coordinates, which I still need. I was hoping for estimated X, Y, and Z.
2. I tried your suggestion and added a marker to the project tree, then placed on the photos. However, when I export the markers I have the same problem and have no X, Y, or Z information. I'm using the "export" icon and selecting "markers" in the dialogue, leaving all options checked including "save estimated values."
You are right that these two options seem to have the same end result.
I still want to know what the coordinates are in model space (local coordinates), based on the geometry that Agisoft generates. I realize they are not real-world coordinates since I'm not adding coordinate information, but that's sort of the point.