Nevermind, this seems to be a regression in box64, I've just found an old version and everything works. Sorry for wasting the time of anyone who reads this.
Although having an arm64 GNU/Linux version would be really cool.

I've been successfully running a headless server on my Raspberry Pi 4 Model B through the box64 emulator at least until version 1.1.100, but now I'm running into issues at this step of the startup process 4.216 Info HttpSharedState.cpp:58: Downloading https://auth.factorio.com/generate-server-padloc...