I think the confusion here is that Signal does in fact encrypt the notification in transit [1]. The FBI had access to the user's unlocked iPhone and went through the notification history on the device. The issue the user faced is that even though they deleted the signal app they were unaware that iOS (and Android by default) retain a database of past notifications even after they're dismissed from the notification pane.

[1] Well actually they just send a blank notification, the signal app then reaches out to the signal server for the actual encrypted message content when it receives the empty notification.

I'm sorry but I'm having a really hard time understanding what you're saying. The first sentence I cannot understand at all. As for the second sentence, I think you might be confused about my usage of the term "Alphabet boys", which is slang for the intelligence agencies: https://youtu.be/lLf84LPzlVc?t=61 it seems like you thought I was referring to Google's parent company.