I ran into my share of flatpak woes around steam, pressure vessel runtime and trying to use Mesa 22.x just this weekend. It’s good people are posting what they’re doing to fix these issues since I was going in almost completely blind for my own as well.
In terms of spotify specifically, you can just avoid the app altogether if the web experience is good enough:
Comment=Spotify in browser.
Exec=/usr/bin/chromium --user-data-dir=/home/your_username/.config/spotify --app=https://open.spotify.com
I ran into the same issue with spotify using a xprop script. I have a keybind to toggle the window decorations of the active window. If you remove the window decorations of spotify, then close it, making it save that state to disk, it becomes unreversable. The only solution was to do as OP and modify the saved state, which in my case was to wipe it.