PilotWings 64 was made by a separate company (Paradigm), who used a very different structure for their games which feels a lot more "western" to me (the UltraVision 64 "engine" has a large structured data chunk which it reads a lot of stuff from; most Nintendo 64 games don't really have that sort of structure)

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.

It was a heavily modified version of Mario 64:

"Miyamoto: We were using the Super Mario 64 engine for Zelda, but we had to make so many modifications to it that it's a different engine now. What we have now is a very good engine, and I think we can use it for future games if we can come up with a very good concept. It took three or so years to make Zelda, and about half the time was spent on making the engine. We definitely want to make use of this engine again."[1]

[1] https://web.archive.org/web/20040619165414/http://www.miyamo...