I agree fully with the use of the replacement cue for the opening, as it's more sinister and subtle. The original wasn't right for establishing the darker, more serious mood the film intended to be.

The scoring process is all trial and error, as a film can take on a whole new personality with music applied to it. It can literally make or break a film's tone, turn it from a serious story and world you believe into just a 'movie' and a lot of the time revisions are made to get the right mood, the right atmosphere.