Recently discovered this. Molly supports link with existing device just like on signal desktop. It even has benefit of getting entire chat history unlike signal desktop. Just restore the signal backup file during setup and then click link with existing device. Then scan with you primary phone. Beauty of open source. Molly: https://molly.im/
If your going to run a independent signal server cluster, you will also need to modify the client applications to connect to your cluster.
You probably would find the molly developers happy to accept a push request to have some configurable backend selection.
Session demonstrates this is possible.
If yo run your signal server does it come with the new quantum E2EE?
Good question, check with the signal github
I don't know man, seems to me XMPP is more secure (unless you trust Signal) and simple to use because you have to jump less hoops
By all means, go with the platform you like better!
https://www.privacyguides.org/en/real-time-communication/
Are all perfectly acceptable options
AFAIK it's entirely done in the client. The server doesn't perform any encryption/decryption other than TLS.