@thedarktangent @brnrd @adamshostack @xabean For this problem space, I've personally CNAME'd the _acme-challenge FQDNs to a consolidated zone, running on a standalone PowerDNS server, and the ACME hook scripts create/delete the TXT records in that database. This supports wildcard certificates, too, FWIW.
Anecdotally, that ACME-validation-only DNS server doesn't even need an IPv4 address.