I'm not super sold on Wine/Proton being the solution to Linux gaming as it still leaves Microsoft in control of the future, but the distinction is quite murky. A lot of "native" ports also use translation layers internally to various degrees.
x86 bytecode isn't the native instruction set on any real hardware you're running games on either, just one of the lowest-level publicly exposed interfaces.
if it's the lowest level available, then it's as close to "native" as we can get, so therefore it has to qualify, if we want to consider anything at all to be running "natively"
Isn’t that moving the goalposts? If an API isn’t exposed for native code then maybe we should just accept that we can’t write native code anymore instead of stretching the definition.