if you fill from the bottom up you will displace all the air. When oil flows from upper hole you can be sure that the gear case is properly filled.
It is more difficult to fill via the top hole and air pockets can easily be trapped. You will more than likely spill more oil and make more mess trying to fill via the top hole.
Having said that I sometimes use this syringe to fill a small gearcase via the top hole but it only holds about 60 cm? so would not really be practical to use for a large gearcase.