The B.L. problems have nothing to do with this design feature. The number 2 engine on respective DC10/MD11 is the same as number 1 and 3 and can be transfered to pylons number 1 and 3 if needed.
The B.L. problems you refeer to was more of a certification problem regarding x-wind/airflow. The S-duct feature on the Tristar was a bit more complicated from a designers point of view, but on the plus side, engine change/acces was a lot easyer than on the DC10/MD11.
The little tap you refeer to on the Tristar's number 2 intake was fitted on the -500 model series due to shorter fuselage. My gues is (and I am only guessing here
) that it was neede due to the intake beeing closer to disturbed airflow from wings, and if the aircraft needed to meet requirements in the whole flight envelope (stall, x-wind, highspeed buffet etc...) this little tap was needed.