The utility on the floppy disk that interacts with the device uses the AmigaDOS "run" and "date" commands according to the docs. I can't think of any reason why the Amiga 4000 wouldn't be able to communicate to this thing, but if there's differences between the 1.x run/date commands and the 3.x ones, or if the utility won't run on 3.x at all, then you might have a problem.