The article mentions that the Main 2D Engine had a mode that could write to a framebuffer that was the combined area of both screens, and could pull from the 3D

The article mentions that the Main 2D Engine had a mode that could write to a framebuffer that was the combined area of both screens, and could pull from the 3D engine into that full framebuffer layer. Also, you'll notice in the New Super Mario Bros example that many of the sprites were pre-rendered 3D and the 2D engine was just pulling bitmaps at that point. So a bunch of options with all sorts of interesting trade-offs and it would be interesting to see breakdowns of specific games and how they used the trade-offs.