Yup, looks pretty normal. htop includes process threads in its output.
A ps -efL | grep syncthing includes process threads (columns 2, 3 and 4 are the PID, PPID and LWP). Syncthing forks a child process, then both parent and child processes spawn multiple threads (I haven’t looked closely at the code, but I’m guessing it could be one thread for each watched Syncthing folder plus threads for other tasks).
A short summary someone in the future might appreciate:
the “Syncthing visible twice for nearby devices” part was caused by two coinsiding, user and system level Syncthing services running. Choose either or and if you’ve already started one and want to switch to the other, make sure to stop, disable and delete the running service first.
the “ID changes on reboot” part was caused by overwriting of the config.xml by the (superfluous in my case) system level service that got started on reboot whereas the user level service did not
the user level service did not get started on login due to the /home folder being encrypted with eCryptfs. The solution was to autostart syncthing by the dekstop environment / wm instead. This is also a safe method of autostarting if one wants to avoid Syncthing ever seeing and syncing encrypted files.
With that this case is now solved, thanks a lot for the help!