Wine/Proton is not an emulator, it doesn't emulate a console nor architecture. Yuzu does emulate both an architecture (ARM on x86) and the console. It then requires dumped games and and system firmware to run, which are not freely distributable.

Wine/Proton is a community implementation of the Windows APIs for Linux, it uses no Microsoft code nor needs any. It runs binaries that Valve already has permission to distribute (the games).