I also don't like that Signal relies on phone numbers or a QR code from a phone to log in. Phone numbers are traceable to identities. They really should have used usernames or e-mail addresses.
Also, Signal's desktop app shouldn't require a stupid phone app to enable it. I have a big powerful setup on my desk and you're asking me to go around my house looking for a silly 6" device to give it permission to log in? That's backwards. It should be the other way around if anything.