I really don't think you can refer to these games as using different 3D engines. The 3D capabilities are ingrained in the N64. The SNES likewise didn't have any

I really don't think you can refer to these games as using different 3D engines. The 3D capabilities are ingrained in the N64. The SNES likewise didn't have any 2D engines (except maybe for when the extension chips were used). Perhaps what we're talking about are the game logic engines.