I wish there was a way to lock the passphrase in the session keyring, with syncthing only sending files to untrusted devices if the keyring is unlocked.
A "password manager" provides a defined api and schields the password away from everything. It can also ask the user if process x can access the key y.
* Do you trust the hardware
* Do you trust the OS
* Do you trust the user
* Do you trust the software
On a rootkit you don't trust the OS anymore. So a safe location inside the OS space isn't an option anymore. But often you are not a root user (e.g. android, windows in a corporate environment)
If you have OS backups there is a risk it is readable by others (e.g. cloud, different IT department). There is also a risk a user uploads the config somewhere.
If you want to rotate keys you would have to search all keys compared to a centralized location.
This would allow syncthing to start at boot, but untrusted devices would start in paused state. Once an external process connects and provides the passphrase (libpam module for login integration?), syncthing would start syncing devices which require the passphrase.