Axles with flats make for easier track nut tightening since the axle doesn't just spin on you. But the different slot width does more than that. Partly there's an historical element to it, but today it makes it easy to differentiate 110 and 120 equipment so there's no confusion at the track.
It makes me wonder how much NJS pays attention to customized parts. I pulled apart a Nagasawa ridden by Nakano many years ago. It had a titanium bottom bracket axle and front hub axle, the headset races and cups had been machined down, and the part of the stem that inserts into the fork steer had been cut down. I've watched bike inspections at keirin tracks and there just isn't that much attention paid to the detail -- they don't dismantle the bikes when they apply the sticker. I've seen the same kind of stuff on a couple newer used keirin bikes as well. Plenty of small trick components if you keep your eyes out for them.