I seriously doubt that Obsidian left the cut scenes there for modders to fix. It seems far more likely to me that the files were left in as a result of their lacking schedule. You don't seem to realise that just because it is possible to mod the game you shouldn't have to mod it just to get the experience you paid for.
By the way, the easy moddabilty (for lack of a better word) of the game isn't intentional, it's merely a result of the engine being based on the NWN engine, Lucasarts doesn't codone modding with their games.