The toe-in is to take account of the bow wave of the airflow off the nose. The intakes are also angled to present the airflow at a better angle in the cruise.
The pylons (on later a/c) also 'droop' to help with the presentation of the engine/intake to the local airflow and to help with the rotation 'mush'.
BTW this was most noticeable on one of QF's 747 classics that had a -400 pylon installed in the no3 position, after it was damaged when the r/h WLG failed on taxi in FCO.
edit to add. The triple 7 also has 'toe-in' on the engine/pylon as well as a quite pronounced angle on the intake for the same reasons as above.