There's only one physical change that I could pick out, and that's where the second right-hand corner straightens out early to meet up with the real circuit's next right-hander, skipping the first left-hand corner of the S turns. The remaining changes seem to all be alternate routes, with the original pavement still in place.
Maybe SMS intends to offer most of Suzuka as an optional layout (apart from that change at turn two), and the default layout has those extra changes to keep relevant parties happy?
Honestly, I wasn't aware that you couldn't model a replica of a track without licensing it. I thought only certain details were disallowed, like advertisements or landmarks.