Hello CindyFr,
Georeferencing procedure (clicking on Update button on the Reference pane) is applying Affine transformations (Scale, Rotation and Translation) to minimize the errors on the checked on instances of the Reference pane.
If you optimize the camera alignment, PhotoScan uses both coordinates of the checked on instances of the Reference pane and also the projections of all markers. During the optimization procedure the relative orientation of the cameras would likely be changed and also the interior orientation parameters would be adjusted.