The Spirit 4k should not have any problem to capture a complete Super 35mm image. Under the Sizing Data tab on the Spirit 4k panel, are controls for zoom, pan, and tilt. I would suggest trying these. In CCD "test" mode, the 4k can capture 4112 pixels, though I've never seen anyone use this mode for production work. No pixels should be getting cut off on the edges. The Spirit 4k User manual has charts that detail the various format sizes.
The Scanity film scanner native resolution is 4300 pixels, so It is also capable of overscan like the Xena, Director, or Scan Station.