I looked on the liner notes to Martha Meet Frank etc. (yes, I own the soundtrack...) and the song was published in 1998 and was mixed and engineered by Alan Douglas, the same guy who mixed most of WAYGTDWYL. So I don't think it was a leftover from the Evergreen sessions. But I wouldn't be surprised to find out that the band just recorded a song that Ian had written already.
I do recall that the song was purposely recorded for that movie with the idea that the movie would be a blockbuster and propel the group into the next stratosphere of stardom.

Obviously, none of them read the script before getting that idea. Interestingly though, Donnie Darko did a lot more to further the Bunnymen cause with their usage (at least in the original version of the movie) of The Killing Moon.