I'm curious if it has to do with the different "stuff" Kawasaki decided to hang off the crankshaft at different points in the model run. I know the A3 had the ignition pickups in the right side, and certain later models added a second stator on the left (with an appropriately thicker sidecover to go over it).
The A1-A2-A3 versions of KZ1300 can be fitted with the same engine guards. A4 needs spacers on the left side to fit the "standard" guards. I have them on both of my A4s.
The European Z1300s can be fitted with standard guards.
The ignition model ZG1300 requires wider guards.