Hello andrey.d,For me it looks like the camera orientation angles loaded to the Reference pane is incorrect - so the model orientation in space in also incorrect. I've input very large number as "camera accuracy (deg)" to the Reference pane settings and then Updated the Reference pane - the orientation of the model after that looked valid.
chunk.camera_rotation_accuracy = (1E5, 1E5, 1E5)chunk.updateTransform()
Hello Mak11,Can you provide the sample dataset were you are observing the problem to support@agisoft.com?Also please specify if you are using exactly the same parameters for alignment.