Hello Raphael,
Export orthophotos feature allows to save individually orthorectified images (images projected on to the mesh/DEM surface) on disk, whereas Convert Images option allows to save undistorted (or distorted images) using the parameters from the Camera Calibration dialog.
Export orthophotos option may give you different distribution of the pixel color values, if the surface used for the orthomosaic generation has holes in it - in this case some parts of the original image could not be projected and will not appear on the orthorectified image.