Yet one more attempt. I have a copy of an old Kawasaki part search software for windows. Looking up 11011-065 and 11011-1006, it confirms that both were superseded by 11011-1025. This should confirm that 11011-065, 11011-1006 and 11011-1025 should be completely interchangeable.
Unfortunately, those old part numbers are no longer associated with any specific model in this software, so I still don't have any way to figure out which part came on which model.
It's also possible that this was actually a running change during production and may not be model specific. Who knows.
The reason why I care is that I have three Z1Rs, and none of them came with the original airbox. I'd like to find the "right" one to replace them with, but I have not been able to figure out a way to be certain which type is correct.