I’m self hosting both too. MollySocket’s docs are pretty clear that it never gets an encryption key for your account, so it can’t read your messages. It only gets/forwards alerts that something happened on your account AFAIK. So I’m not sure what data it has that’s worth encrypting.
For Signal/Molly, it’s less that the notification is encrypted as I understand it. It’s more the notification content is just “Hey! Stuff happened” for Signal. The app then reaches out directly to the Signal servers to see what’s new. So the message content is never sent via the push notification service (UnifiedPush or Google’s service).
The UnifiedPush server is intended to be a single source your phone can keep a persistent connection open to, rather than needing a connection per service/app (this is how Google’s Firebase notifications work too).
As Signal doesn’t support UnifiedPush, MollySocket keeps a permanent connection open to Signal’s servers to listen for new activity and forward them to your UnifiedPush server. This saves your phone keeping a permanent connection open to Signal’s servers and draining your mobile battery more.