You need to install syncthingtray-qt6 (and may uninstall syncthingtray) as I mentioned in my last summary about recent changes in this forum thread. Checkout the remarks in the pinned comments on the AUR for further details.
And yes, this is about the Plasmoid vs. the stand-alone version. Checkout the according README section for details.
That’s fortunately not how it works. When uninstalling a package of a GUI application like Syncthing Tray the configuration is not lost. So when installing the package again you won’t have to reconfigure anything. This also counts for switching from syncthingtray to syncthingtray-qt6 except that you’ll have to remove the “old” Plasmoid and add the new Plasmoid because for Plasma these are distinct Plasmoids. Removing/re-adding the Plasmoid does not reset the overall configuration so this is not a big deal. Again, checkout the README for details.