The buttons are different; on the JP pad the labels ABXY are recessed into the button itself rather than inside the clear plastic. The cord is way shorter and made of a clear green plastic. The analog stick plastic feels different too, it has less texture (and it’s not from wear).
The XBOX jewel logo is obviously different but there are a few other logos changed or missing like the Microsoft logo doesn’t appear anywhere on the JP one. It’s pretty clear they did another plastic mold for the S controller.