How could it? It works by examining packets of control connection, reading commands and responses, changing addresses and ports in them, using that info to recognize data connections. If control connection is enrypted, it can’t do any of that.
No, linked page is about something else. It says that previously, encrypted connections were blocked, because the helper was apparently too nosy and didn’t like AUTH command. Now it doesn’t do that. And it seems to be meant only for client use, because it says that only passive connections work (they are simple outgoing connections, no special treatment is necessary for them). But active ones (where server connects to client) still don’t. And can’t because for that it would have to be possible to read control connection.