Hi!
You can run following command in python console before building an orthomosaic:
Metashape.app.document.chunk.transform.matrix = Metashape.Matrix.Diag((1,1,1,1))
The reason you are getting this error is that project is not referenced and model coordinates are considered unknown and thus can't be tied to marker coordinates.
Code line mentioned above sets project to use these internal local coordinates. Note that all measurements will be still invalid, since internal coordinate system is arbitrary.