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I looked into this recently.
There's a DNS challenge designed for this exact scenario called (from memory) DNS01, but it's more of a faff than I'm willing to get involved with.
Basically you push proof that you own the domain into a DNS record instead of to a file on a web server. It requires a DNS provider that has an API and a client that speaks that API.
It also leaks private DNS stuff into the public domain.
I'd love it if someone devised an easier way. Maybe there is an easier way?
I do the dns challenge with letsencrypt too but to not leak local dns names into the public I just run a pihole locally that can resolve those domains
The DNS server is only one thing you tell the domain, the other is the certificate authority. And those publish all issued certificates as part of certificate transparency. https://en.m.wikipedia.org/wiki/Certificate_Transparency
To mitigate the amount of published information, you can request wildcard certs to keep the subdomains private.
You can also use a wildcard cname entry to capture all subdomains and leave out the pihole faff, given that you use a reverse proxy that forwards to respective services by subdomain.
Yep I also run wildcard domains for simplicity