Thanks for the clarification, guys. I was totally wrong, then, -- I assumed that this script compiler was used by the game to hold dialogs, since in them actions and triggers are not compiled
Those in BIFs/override are used by the game and all relevant modding tools, including WeiDU. The script compiler folder is, hence its name, only for the old compiler.
The stuff in the "script compiler" folder isn't used unless you are using some seriously obsolete compiler. Differences between the IDS files are most likely because the IDS files in the "script compiler" folder are themselves obsolete.
My 2nd question is, such .IDS files, -- are they supposed to be 100% identical, evah? The fact is, some slightly differ. Is it OK, or are all such differences caused by errors?
The IDS files in the BIFs/override folder are used by the game. The ones in the script compiler folder are for a separate compiler that was released sometime after the game, as far as I recall.