Xbox 360 controller on PC

[Atomic_Skull]

It would be, because AFAIK that requires the newer input standard used by the xbox controller (Xinput). FFXI uses DirectInput (part of DirectX 9 and earlier) for gamepad support, so functionality which depends on Xinput wouldn't be available. Newer games that support the xbox controller specifically do not support a lot of older game pads because they only use Xinput, not DirectInput, which is now considered depreciated by Microsoft and will no longer be a part of future versions of DirectX.

FFXI for PC doesn't use Xinput, thus it will not fully support the xbox 360 controller under Windows.

No it wouldn't, the shoulder buttons show up as an axis in Directinput. It would not be hard to make FFXI able to recognize an axis as a button. From a programming standpoint it's not hard.

(The Xbox 360 itself is another matter, because it's not Windows)

Actually the Xbox 360 is windows, just not Intel Windows. It runs a PowerPc version of Windows and DirectX 9. Porting applications between the PC and Windows is basically just a matter of cross compiling the application.