Proton is not an emulator, it’s a compatibility layer. They don’t try to emulate Windows system functions, they just translate Windows system calls.
They make a difference, legally, since compatibility layers don’t recreate any functionality from the original process, while emulation recreates the internal operations of the system.
Regardless, emulation is legal. I wonder about the legality of this DMCA; Yuzu is open source, so there’s no copyright infringement on their code, right? It’s licensed under an open source license. And there’s no Nintendo code being copied, nor Nintendo assets. I’m not a lawyer (or even American), but I think this is DMCA abuse.