it's not possible to accurately reproduce the Sega Saturn in Direct3d and thus the slower but lot more accurate software rendering is used, the author mentions that on the main page (at the bottom).
The Saturn used forward-rendered quads, while Direct3d uses polygons, they work entirely different.
Personally, I think it's a lot better that it uses software rendering, even if its slow. The image is reproduced 1:1 this way, even up to the level of interlaced drawing (!!!) which is something that I haven't seen in too many emulators. Are there any psx or n64 emus that work the same way, by the way?