Earlier quoted context omitted.
I tried this too a couple months ago, OP is right, certbot doesn't support the CNAME aliases: it lacks logic to add the TXT record to the redirected name, instead of the name in the certificate. I use acme.sh which does support it: https://news.ycombinator.com/item?id=47066072
I still find this hard to believe without some actual example RRs and certbot configs, but this is HN, not serverfault.
...but they also don't say how to specify the zone to be updated like acme.sh does: https://github.com/acmesh-official/acme.sh/blob/master/dnsap...
So say you want a cert for *.foo.com, and you have:
_acme-challenge.foo.com CNAME _acme-challenge.foo.bar.com
...I can make certbot talk to the foo.bar.com DNS server, but it tries to add the TXT record for _acme-challenge.foo.com, which that DNS server obviously rejects (and even if it accepted it, that obviously wouldn't work).I'd be happy to hear there's a way to do it that I missed. Also I'm specifically talking about the rfc2136 support, maybe some of the proprietary certbot backends do support this.
EDIT: Here are more references:
https://github.com/certbot/certbot/issues/6566