When I go to submit my recording, the only option under platform is "PC" and there's a message "Emulators are banned".

What does that mean exactly? I use the Steam version on Linux - so technically I'm running on an emulator? (Proton)

you are using a pc - the selection fits your run

Just for the record, even if it doesn't matter. Factorio has a great native Linux version, and it is in on Steam. So you are most likely not using Proton when playing Factorio on Linux.

And even if you run factorio trough wine -- it is in name: Wine is not an emulator it is runtime library wrapper. Binary does not know that it runs in different enviroment becouse that enviroment more or less (definetly more) mimics real windows library (dll) behaviour, up to point you can choose whitch windows version it have to mimic