They are different, if you run the first track in a Yakuza port vs MAME, the corners are different.
Sega did the same thing in the original Hang-On, leading to people saying the version of Shenmue 2 HD was a new course, see my video on that here:
Basically, at some point, Sega switched from using the upright version of the game (as in the Dreamcast original) to the ride on version (which is what Ryu plays in game)