To me that wiki sample of flanging has this cool ominous sound - any chance it could have been done on purpose in that scene?
No, not a chance. That music was not designed to be heard like that, as evidenced by the soundtrack albums and collections themselves. If it happened that way on the CD, LP, cassette, reel to reel, or 8-Track, then there would be no issue. Although I must admit it still would sound out of place if it was meant to sound that way. I just wish there was a print somewhere that didn’t have it. But even if they existed then, they likely wouldn’t exist now.