The teflon tape is a solution to address creaking bottom bracket. Sometimes the tolerance difference between the threads machined into the frame and those of the cups is enough to cause clicking or creaking and folks have reported succes in eliminating the noise by putting a couple wraps of teflon tape on the cup threads prior to installing. Be sure to wrap in the direction that would cause the tape to further tighten when screwing in the cups (for english threaded cups the tape should wrap CCW around the non-driveside and CW around the drive side).

Don't sweat that lip on the plastic cup as some models don't come with it at all...the purpose of the non-driveside cup is to establish support for the cartridge in the frame without any play along the length of the bottom bracket inside the shell...it has no effect on bearing adjustment. Make it as tight as you can without damaging it and then bolt your cranks on and log some miles.

If it will make you feel better your LBS might have a spare plastic left side cup without the lip they can toss you or you can order a metal from Problem Solvers...Problem Solvers

But in my opinion your worries are causing you to look for a solution to a problem that does not exist.

-j