You could try to run: sudo ~/mailinabox/management/ssl_certificates.py
Oh, and by the way, if you do indeed check the fingerprint of the self-signed SSL certificate before connecting with your browser, hopefully you also checked the SSH fingerprint before connecting with an SSH client, otherwise you can’t be sure that the CLI you are connecting to is actually that of your own server.
I think the reason it is done this way is because MiaB is meant to be easy to set up, even for people with little knowledge of DNS, which is also why it comes with an authoritative DNS server, so it can handle the DNS for all your email domains for you.