My understanding (i.e. random guess) is that since the outer button is more accessible to your finger, it makes sense to make that button the "main" button and the other button the errr... "other" button. This can be most apparent during decision making, that you "confirm" with the outer button and "cancel" with the inner one. So it seems natural to name the outer (main) button A/I, and the inner button B/II. It would be a bit awkward to press B to confirm and A to cancel right? (I think such games do exist though.)
However, in "western" sense it is also reasonable to have the confirm button on the left and the cancel button on the right (as seen in options of questionnaires, etc.). The problem is, when you press the buttons on a game controller it doesn't feel so well in this way.