As for Sony, they noted in a recent statement that there will be no way to alter this command option, but they offer no official explanation regarding why they made this change in the first place. It seems logical that this is based on their desire to unify the platform across all regions, but until they offer an official explanation, we can only really just guess in regards to their intentions.
In any case, it seems that Nintendo is the last major “hold-out” of the old “confirmation input on the right” layout, which (if nothing else) is an interesting footnote in the evolution of the video game industry over the last 30+ years. As gaming becomes more and more global and the lines between regions. and even platforms, become blurred, we suppose we can see the logic in changes like this helping to unify concepts across the board.
Still, it would be nice if Sony offers some kind of way for Japanese gamers to swap the inputs. At the very least, this swap will surely be an inconvenience for many gamers in a market that has traditionally helped Sony maintain the hardware lead over Xbox in the three previous console wars the two companies have engaged in so far.