Right, I've actually stumbled on a solution to both issues, so to save other people the bother, I'm going to outline my findings.
This issue is actually down to there being override folders and swkotor.ini files in duplicate locations due to some quirk with how steam downloads the game (replacing the swkotor exe with an OSX app file)
With the swkotor.ini file, rather than being in the game folder in 'Steam apps', it's actually located in its own folder at:
'your username'/Libaries/Application Support/ Knights of the Old Republic
When it comes to the override folder, you need to ignore the first override folder you see (in the game folder) and instead, right click on the 'Knights of the Old Republic' app file and select 'Show Package contents'.
This app file has its own file structure within it which includes the actual override folder, making the 'leftover' ones in the main folder completely redundant it seems.
Hope this helps others in future!