Someone came up with a discovery that's a bit odd.
The preset (E) that we use would normally work, but we have Confirm and Cancel reversed (JP style).
JP people get the opposite issue it seems, they get Confirm and Cancel reversed too (West style).

Now... what would happen if we were to go into the Japanese TOOLS folder, copy the xinputdll.dll file that's there, then put it into the TOOLS folder of our specific region AND in the default FFXI folder? (make a backup of the original files first!)
If this works, and that's a big if, the result could be a preset E with confirm and cancel placed on the position we expect them to be.


We would still be left with the issue of being unable to customize the presets though, there's no workaround to that until SE patches it.
Personally I'm gonna stay with my temporary workaround until SE releases a fix, but if someone else is feeling optimistic and wants to try this small test then feel free to and post your results!