I've just come across this page and found that there is a bit of confusion about a few things so I just wanted to share a few thoughts/experiences with iOS users interested in modding this game..
Firstly: Use iFunbox or a similar program to make the transfers easier - forget SSH and other awkward methods - It doesn't have to be that hard!
The Override Folder
What happens, it seems, is that the override folder is a mixed bag - TGA and Model files seem to affect the game in progress (you can change the files and then reload and you will notice the differences - although I usually get a crash or just black textures so far)..
BUT mods like Jedi companions (which are edited UTC files I think) DO WORK but only when you start a new game = when you start a new game a bunch of files are compiled from the override/game folders and put into your documents folder (currentgame/gameinprogress)..
When you change the overrides after the start of the game the changes will not happen in the current saves because things like the character stats (utc files I think) have already been copied into the USEABLE part of the game folder structure (IE NOT THE KOTOR.APP which is supposed to be read only) - the Documents folder is where all the current-game info is stored because it's a read-write folder.
When you jailbreak the device it means you can access and modify the actual game-folder so putting new files in the override folder requires a jailbreak. HOWEVER - if you have these save files already, then you can install them directly into a non-jailbroken device and play with your modded save-game (for example I did this and still had an all-jedi party and even still had my special Revan robes! which surprised me actually)..
So it seems that the main point I'm trying to make is that mods seem to affect the game only at the start of a new game - whereas texture-mods (which I haven't gotten to work yet) aren't stored in the actual save folder..
I'm not sure if permissions affect anything - they weren't needed for me.. The override folder is read-only on a JAILED phone and read-write on a Jailbroken one. I could be wrong but I never had to touch any permissions to get the mods working. The main thing was to start a new game so that the documents folder is populated with the new overrides.