The other player who tested in Fedora gave me a hint at what the issue might be - are you using the X or Wayland graphical display server? I'm going to be honest I barely know what those are, but this person thinks that if you're using X that might be causing the issues with changing window size.
Viewing post in Hitches every few seconds in Linux (Manjaro 64-bit)
Yes, I am using X. Wayland is the newer, much more modern display server (drawing and managing windows, handling input, etc) that isn't supported by Nvidia yet, I'd be running it if I could. Most Linux distros do not enable it by default because of various compatibility issues (though the hope is that will change in the next couple years). If I had to guess I'd say a majority of people running Linux games they bought on itch or Steam are still using X.
One thing I was able to do is edit package.json to change the starting size of the window to 1920x1080 (my monitor's native res). This gives me a 3x scaled (1440x810), centered view when the window is maximized, which while not ideal is just about good enough to be playable. That result is obviously pretty different from what you'd get setting the resolution from within the game's code, but maybe that's a starting point for troubleshooting if more players report this issue. (and if not, great!)
Thanks so much for the help troubleshooting!