Signal basically sends "empty" notifications to FCM, so Google can't read the messages. When your phone receives a notification for Signal/Molly, the app is woken up, it fetches data from Signal's servers, then displays the notification.
And remember that Signal/Molly messages are end to end encrypted. Even if there were a 3rd party that could intercept messages, they wouldn't be able to read them.
The way Signal's WebSocket push notifications feature works (as far as I can tell looking at the server code very fast) is Signal/Molly just connect directly to Signal's servers and maintains that connection so it can get messages as soon as they're available.