Well one example is for a 35mm feature I was shooting this fall, the production bought a DVX100A to shoot any behind-the-scenes footage, but also so I could shoot any fake news material to be played on TV sets in scenes (the movie had scenes of the media gathering at this family home.)
The behind-the-scene stuff was shot at 24PA with a letterbox, but my fake news footage was shot a 60i in 4x3 full-frame. So whenever I borrowed the camera from the behind-the-scenes guy, I had to switch to a different Scene File.
You could also set-up the Scene Files so that the frame rate was the same, but some files had different Gamma presets than others, or Cine-Like Chroma was on or off, etc.