I use an xbox one controller and my 'Xinput' is unchecked and it works fine.. but yes.. a real pain to get to work.
with native drivers: it doesn't.
Note: working for you =/= working fine.
but as far as OP: there's a couple things, but the main thing is to make sure you run the gamepad config for the client you're running. Assuming you're using windower, in the profile settings you can select "auto-detect" or at least in my case "North America" just select the client you're definitely running. Then make sure you're running FFXiPadConfig.exe int he ToolsUS directory. Next apparently you want to make sure your windower directory isn't in your game directory at all, put it elsewhere. Can try reloading the driver, then verifying x-input is checked (xbox controllers are xinput devices, not directinput, and unless you're using a custom wrapper for it then it is what you want selected (used to be necessary to use a wrapper to get it to properly work for xinput devices, as XI didn't use to natively support xinput devices).
Major known issue over the years: M$'s win10 auto installed driver was incompatible, had to manually reinstall the xbox360 controller for windows pack after deleting the driver, depending on your version of OS this may be the root cause, I don't believe they've changed that driver yet, then again I have never tried setting up an xbone controller on the PC yet.