Just my 2p's worth here but I understood the larger intake on the No.2 and its positioning above the fuselage was:
a: To allow sufficient air to enter the intake (more powerful engine) but with out ingesting any B.L. (see below)
b: To negate the Boundary Layer on the upper fuselage mixing with the intake airflow.
The B.L. was a significant enough problem on the Tristar that they fitted a smoothing fairing between the fuselage and intake to No.2. Obviously the designs are quite different but a similar issue would have been at play on the MD-11.