It is correct that MiaB sets up a single dns server that is reachable through multiple dns entries. As you note, this is not good enough for some top level domains, where a requirement exists to have at least 2 different name servers.
The Secondary DNS functionality supports this by enabling external slave dns servers to act as a nameserver for MiaB. The DNS configuration is then synced to these secondary servers. You can provide the secondary servers as nameservers to your domain registrar.
See here for a better explanation and tutorial Setting up Secondary DNS for Mail-in-a-Box
I think port 953 is used by named (bind9)