For Linux-native games (there aren't many) it uses what I described, making the system look a lot like Ubuntu to the game. Proton is for Windows (PE/exe) binaries, not Linux (ELF).

Jonathan Blow is sharpshooting and being intentionally difficult in order to sound smart (he really needs to engage in that behavior less, he's smart enough as-is). Virtually nobody bothers with Linux-native binaries for games. Compile your game for Windows, test it on Linux+Proton, find that it probably works fine, it's not hard.