Its quite easy to prove that libdragon was fully clean roomed. There are thousands of proofs like the git history showing incremental evolution and discovery, the various hardware testsuites being developed in parallel to it, the Ares emulator also improving its accuracy as things are being discovered over the past 4-5 years. At the same time, the n64brew wiki has also evolved to provide a source of independently verified, trustable hardware details.
Plus there are tens of thousands of Discord log messages where development has incrementally happened.
This is completely different from eg romhack-related efforts like Nintendo microcode evolutions where the authors explicitly acknowledge to have used the leaks to study and understand the original commented source code.
Instead, libdragon microcode has evolved from scratch, as clearly visible from the git history, discovering things a bit at a time, writing fuzzy tests to observe corner case behaviors, down to even creating a custom RSP programming language.
I believe all of this will be apparent to anybody approaching the codebase and studying it.
The Wikipedia article on clean room reverse engineering has all the examples that came to my mind and then some. https://en.wikipedia.org/wiki/Clean-room_design
With what evidence?
In other words, money that these people don't have. The legal system is not a solution for these kinds of problems, nor it is affirmative defense. Anything that makes the defendant bear the burden of raising and proving that their actions didn't foul any legal requirement, is basically killing any project, even when using your "solution".