Hi SHJ,
The transmission/reception pattern of a VHF quarter-wave ground plane aerial can be imagined as a flattened doughnut around the aerial, therefore the performance of such an aerial when the aircraft is flying well above the elevation of the ground station is very similar whether it is located above or below the fuselage. In other words when the aircraft is in the cruise, talking to an ATC station 100 miles away, the path to the ATC aerial from either fuselage location is nearly identical.
However, when the aircraft is on the stand, it will have all sorts of clutter around and underneath it such as steps, refuelling rigs, baggage trucks, catering trucks, air bridges and buildings etc. etc., and in this case the aerial above the fuselage will suffer fewer reflections and obstructions and probably perform better.
VHF transmissions do not need to be direct line of sight clear, but satellite transmissions do.