I think there is realtime 3D used for the player and enemy "sprites" (really 3D objects), including the end of stage bosses. They are small and extremely simple, as this was the maximum the Genesis/Megadrive's 68k CPU could handle. The final boss fight is the exception.

Silpheed was amazing back in the day. It was one of the first titles that really showcased what CD drives could add to games in terms of cinematic experience. The live orchestral music gave it an epic feel and the mecha-design of the SA-77 is beautiful and modern even by today's standards.