I am not sure why that distributor was different but I went to the shop I got it from and swapped it and pointed out the difference. He too was baffled.
Simply put, this is the rotor that is supposed to fit on there. Where the screw is supposed to go, there was no hole on that side opposite where the end was flat. The new distributor I got has the hole going all the way through.
Maybe some Japanese prankster desided to change it before departing his or her car. Anyways, I hope it is going to run now.