I mean to only use MiaB DNS server for only the domain that is only used for only being a mail server and is not used anywhere else for any other purpose on any server anywhere.
If the domain for the mail server is example.net, then that domain is only used for the mail server, and does not exist any other place.
If you are concerned about the vaporization of the server from all existence, then you are going to suffer this issue in regards to backup of mail on the server that most users use exclusively through IMAP, so if you have no backup plan for your mail server, and you are concerned about this, then, from that perspective, you are assured to lose everything, anyway, and users will likely be more angry at you for losing all of their mail than the DNS being unavailable for some short period.
As for domains that are served from a web server some place else, which also makes use of some external DNS, such as Cloudflare, there is no reason to have MiaB DNS server do anything, at all, which such domains, and, just the same, MiaB will not have anything to do with the TLS certificates for such a domain.
From my perspective, you have spent more time trying to hash out an unnecessarily complex configuration than just going to your favorite registrar, shelling out $12 for a domain, use the MiaB autoconfig, make some simple MX record changes on the other domains, then going on with your life.