When running automatic mosaicking in OrthoEngine, overviews are automatically generated for the mosaic. However, this is not the case in your python script. You would have to run PYRAMID after MOSRUN to generate the overviews for the output mosaic. You can also check and generate overviews in the Overview Manager in Focus (Focus > Files Tab > Right-Click image > Overview Manager). Once overviews are generated for an image, the size will increase slightly, which is why the two output mosaics are of different size.
Hope this helps!