A suggestion: Use the same registration method for vertical but use the outer edge of the film for horizontal. Take a look at the gap between your perf and your film frame - see how it weaves back and forth? This is because in Super 8 the perfs are stamped using a 5-perf stamper that is never perfectly in parallel with the film. So you get a kind of sawtooth pattern. If you use the perf in Super 8 for registration, your perf will be perfectly placed but the picture will weave back and forth in a consistent pattern. Not all films exhibit this as much as others but it’s been a “feature” of Super 8 since 1965.
Lasergraphics modified the ScanStation scanner’s registration after we (and some other owners) worked with them to fix it after testing film shot on the Logmar pin-registered S8 camera. The jerkiness was really intense with that camera. Ironically, it’s less of an issue with cheap cameras that have narrow pulldown claws, but the better cameras seem to show off this issue more intensely. What Lasergraphics ended up doing was to use the horizontal (top/bottom) lines of the perf to do vertical stabilization, and the physical film edge (not the frame line) for horizontal. This means pulling the camera back a bit to ensure you capture both film edge and blank space in the gate. if the gate isn’t big enough, though, this won’t work.