> It has went through several cleanup refreshes since then but they intentionally avoid the leaked source in doing so.

As if that would make a difference in how big of a copyright violation all of this is.

Assets are not included in the process which helps a lot, it still requires the original ROM to compile a ROM. Nintendo has heavily went against PC ports, even as far as videos about them on YouTube, but never even attempted to touch the root decomp projects for various titles. Later games you can get into more trouble because EULAs or on screen warnings started restricting reverse engineering, as well as DRM mechanisms which are impossible to reverse engineer without being implicated as also advertising a way to work around them.

Is this clean-room development process the cover story or honest-to-god truth? How does anyone verify that outside of the individuals who worked on it directly?

The decompilation process and toolset made available would take more work to fake than to just do, not to diminish how much work that last bit is. Particularly since parts of the toolset work successfully across many titles (e.g. Paper Mario, Super Mario 64, and Ocarina of Time).

You could download the leak and compare them

I’m sure people have done this, I have the leaked code somewhere so I could do it if you want