The same reason why they're the only ones with purple buttons.
In North America, the SNES came out several months after its release in Japan, giving time for the redesigned controller. Ergonomics and all that.
Why this change wasn't kept for the even later European release, or why the controllers weren't similarly redesigned for Japan, I don't think anyone really knows. Probably a lack of communication between NOA, NOJ, and NOE, or it would've been an inconvenience- the multicolored buttons used on the J/EU controllers might have something to do with it.