The tweecer essentially changes your computer to whatever ECU you want, in most cases, the X2J.
Plug a tweecer into your B9B, tune using the x2j.dat, and your computer will function like an X2J as long as the tweecer is plugged in.
This is the function that the original LPMs had. They could override an older ECU, and turn it into and X2J. A single LPM could be tuned, and work with any ECU.
Ford sued the people involved and won, but the courts decided that even though the ECU operating code is property of Ford, the actual calibration information was free to be changed by anyone.
After that, the LPMs had to be programmed with calibration only, specific to which ever ECU you had. At this point a LPM written for a B9B would not work on an X2J, etc. The ability to override the ECU code, and make one chip for any ECU was gone.
Today, tweecer has the ability that the first LPMs had, so as long as you are using tweecer, it should not matter which ECU.
EDIT: I don't know much about the SCT chip setup, but if the SCT does both calibration AND ECU code like the tweecer, and like the first LPMs, you should be set.