One, there is literally an entire NES test suite ROM specifically for testing emulator compatibility with original hardware. Nearly 80% of the tests are hardware specific quirks that have genuinely no impact on any of the original NES ROMs and emulators can freely omit them to save on performance.

Two, with Linux adding NTsync, it can now act just like the NT kernel that Windows uses. You don’t need to use hardware emulation when you can recompile software or translate syscalls unless you are dealing directly with firmware like NES ROMs or HID drivers. Wine and Proton basically just act as reimplementation of the WinAPI and can often be more faithful to the original implementation since they have built-in tweaks dedicated to each software where the WinAPI has been free to make breaking changes.