Looks like it may be in $HOME/.var/app/io.itch.itch/config/Leone Gaming/Upheaval for both systems. Still haven't gotten the saves to sync, but I think it's a permissions issue with syncing method I'm using.
So far the Steam Deck experienced has been incredibly smooth. I just installed it via Itch and added it to my Steam library. I was surprised to see there was native game pad support (I was expected to click around using the trackpads). The UI and text is all visible and legible. Let me know if there's anything you'd like me to test and/or try. I'll let you know if I run into anything. I appreciate you too!