I thought it worked the same as Whatsapp, whereby there's a sort of backdoor connection to the app running on your phone to send messages.
However, after doing a smidge more research it seems like somehow Signal is sharing it's key with the desktop app and only syncing history of messages directly: https://news.ycombinator.com/item?id=15596980
I'm not 100% sure how it works as the server is fake-open-source and not actual open-source.
But I'm having trouble discerning what you mean.
Either you're saying group chats are encrypted E2EE - which, I never claimed.
Or, you're mentioning that you can have multiple phones/devices on the same account, which doesn't work the last time I checked.