After having to deal with VM hosts that do GeoIP blocking, which unintentionally blocks Let's Encrypt and others from properly verifying domains via http-01/tls-alpn-01, I settled on a DIY solution that uses CNAME redirects and a custom, minimal DNS server for handling the redirected dns-01 challenges. It's essentially a greatly simplified version of the acme-dns project tailored to my project's needs (and written in node.js instead of Go).

Unfortunately with dns-persist-01 including account information in the DNS record itself, that's a bit of a show stopper for me. If/when account information changes, that means DNS records need changing and getting clients to update their DNS records (for any reason) has long been a pain.