UPDATE:
I pulled the Syncthing RPM config folder and removed the layered package using ostree rpm-ostree reset.
After that, I installed the Syncthing Tray Flatpak by marcthus and copied the Syncthing config folder into the syncthingtray folder in the .var/app directory.
I then activated the integrated Syncthing app from the settings (Startup > Syncthing Launcher tab) and also added the Flatpak to the startup apps in the KDE settings.
I switched into Game Mode and, using Decky Loader, installed the Syncthing plugin.
I went through the setup process, selected Flatpak as the service type, and added the ID for the Syncthing Tray Flatpak.
Lastly, I enabled the “Start on Boot” option in the plugin settings and restarted both into Game Mode and into Desktop Mode multiple times to verify everything.
Now I have Syncthing running in both Desktop and Game Mode, regardless of where my first login happens.
List of what I used:
- Syncthing Tray Flatpak
- Decky Plugin: Syncthing