Other apps may provide higher anonymity, but none provide privacy guarantees higher than (or even close to) Signal.
So, being "best" at privacy is meaningless unless you are in the very lucky position that your local jurisdiction fits Signal's threat model. There aren't many in the west even...
Signal has taken measures to limit its ability to know who I'm sending and receiving messages from. Though it's still possible by mapping my IP address to me. So yes there is still a centralized metadata problem, but I'm not letting perfect stand in the way of better.
Not in most cases, for most people, most of the time. Everyone knows you communicate with your family, friends and business associates. Very few people communicate out of those groups and even if they do they rarely have to worry about anyone finding out about it.
- Using phone numbers means that Signal can constantly check against your contacts to let you know if any of your contacts are now using Signal. As such, using phone numbers encourages use of Signal.
- The usage of phone numbers instead of email or usernames also helps combat temporary/fake account creation abuse, as phone numbers are KYC if you ban VoIP numbers
That said, in the end it is a compromise on privacy and anonymity to increase the popularity and stability of the app.