That problem is easily solved at other places in the FS stack. Use an crypto overlay like EncFS and sync only encrypted data. Alternatively, even stream encrypted updates to a directory via a gpg job and sync the encrypted blobs. Another layer, but the script would be so simple it'd essentially write itself.

While it would be convenient to have configurable encryption on endpoints, syncthing is composable, and thus this issue can be worked around. If you have a platform that doesn't allow you to compose tools easily like Android, that's limited technology.