Add a simple notification and logs for service's runs
Since you seems to be doing a lot of changes, I'd like to suggest that a notification system as part of the service's executable, just to notify if there's any issues and where to find the log for any successful/failed runs (I'd suggest ~/.var/log/flatpak as .var is more people are familiar for people using flatpak than ~/.local/share/flatpak).
I'll be honest, for now I've just been going "Yup, this works well enough, I'll wait for a month before diving deep into it again." You seems to be doing a lot of cool things, but I have no idea what's going on for now as I've been a bit busy to really keep track of the changes.
I didn't even know you have an override system now (which is really cool) or about the /var and /tmp limitation until just now...