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.
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.