Possible .batch file possibilties.
Well I was thinking, modders for the Jedi Knight games have used .batch files to have the game load resources from different locations than defaulted to. The best example of this is the Dark Forces mod for Jedi Academy. The mod uses the batch script to allow the game to load their new levels instead of the default ones, while still allowing the normal game to be run simply by clicking it's excuteable.
Would it possible to apply the same effect to the swkotor2.exe and the launcher.exe? TC mods like The Jedi Masters could then make even more indepth changes.