Steam Auto-Cloud has now been enabled, so saves should sync between devices (even cross-platform).
Version 1.04b itself is only for Linux builds as it fixes a major performance problem. I'd gotten the report a few times but had no idea what was going on as I primarily develop on Linux and wasn't having any issues.
It turns out that when you're not using a controller, I was accidentally polling evdev for new controllers to detect every single frame. On my Manjaro setup this wasn't a problem but after switching to Arch I forgot to bring over a configuration patch for my keyboard (it's a long story) and so that device would now seemingly time out when polled, making each frame take 20-30ms!!
Now the check will only happen if the timestamp on /dev/input indicates there's actually been some sort of device change, or if you manually press the button to detect controllers in options. It's still possible the game might lag for a bit if you plug/unplug a controller while playing but it should just be one little hitch instead of tanking the framerate outright. In the future I'll need to just do the check on another thread so it doesn't block like this.
This was also happening on Steam Deck running the native build. While this patch should fix performance on the Deck, I still don't have proper gamepad support set up with it and likely won't anytime soon so for the moment I still recommend sticking with the default Proton configuration.