Just in the same way that the same pickups will sound differently on different guitars.
As you know, tone is a composite of many things: wood, workmanship, hardware, pickups, strings etc.
A similar core scalarizer will sound different on different guitars as well because these factors can never be replicated on another guitar. In effect, it's also like saying that each guitar is really unique and tonally different from the next. Yep...even on anal-quality-controlled japanese guitars.