The original designer could get a taller ship in because he took advantage of the diagonal height of the bottle; making the bottle rest on its edge in the stand.
Lego has chosen to rest the bottle flat on the stand, thereby cramping the available height for the ship - thus restricting what their designers can come up with in that space.
That's just my take on it - don't really know or not if the original model was unstable enough to cause Lego to go with this revised take on the design