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.

Unlike JK we have to change files like 2das, scripts, the tlk file and no other file can have the same name. So not really, the installer cant know anything about the this so there would be alot of things not compatible.

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.

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.

Not that I am aware of. The Jedi Outcast/Academy executable accepts commandline parameters when started where you can set where it loads the game data from, hence it's easy to make batch files to load different configurations. The swkotor.exe executable does not work like that.

One thing that works much like you are talking about is KMM Kotor Mod Manager. It has relatively become extinct in the moddern community because of stoffe's patcher utility. However another option is you could write a batch file to install multiple mods all at once and another to uniinstall. Your batch would simply run the executables for all the mods that use stoffe's patcher and copy paste those files that don't to overide.