Z values are in each tile. It is hard to test, but you can see standard Z values (used in PS version) on the new "Sections" tab in the background viewer (select a section to see the Z-value in the field below). And for the strange PC Z value, I cannot show it easily... almost each tile in layer 1 have a different value.
I modified the editor for AKAO to display the list of "operations". AKAO is different to AKAO2, because the first param is 8-bit, instead of 16-bit. It is possible that affect vars too, but like you said AKAO is never used with variables.