Modern (airliner) design practice of having the Thrust Line considerably lower than the Drag Line has bitten a couple of Crews recently when they discovered that there was a
Vmc in pitch under TOGA Power settings. Presumably a heavy load 'upstairs' in a 380 would make this condition worse under GA acceleration.
I presume placing the Motors where they are gives easy maintenance access and provides a pitch-up moment during cruise (which reduces induced drag). But as A/C get larger and more powerful is this pitch-up moment going to become a problem? Perhaps the 146 with its thrust & drag in the same plane is the configuration of the future