Differences between uncalibrated and calibrated stereo

I would like to obtain the depth map with a stereo-microsope equiped with cameras. If i understand, we can use a calibrated method from the chessboard use and uncalibrated one based on specific points. I tried with the two methods and the undistorded images are clearly different :  I have some difficulties to explain the differences as i used more 30 images per camera in several configurations. The angle between the two cameras is important and imposed from the stereo-microscope geometry but the rotation is very marked on the picture... And i have a final question, for the depth map, the distance is from the lens or the camera captor?