That aside, Let's Encrypt had an exemplary response to this issue throughout, and has made the right call here. A best-effort whitelist will enable a smoother transition for those on some known-good hosts, while mitigating this vulnerability and keeping their cert ecosystem uncompromised.
The work will now begin to add support to the other validation methods in ACME software that's lacking them, and to engage with the other custodians of the ACME protocol to rectify this particular flaw in design.
While the http-01 challenge is the recommended migration path, and likely the easiest to automate with greenfield software, the dns-01 challenge is the one with the fewest amount of intermediate assumptions -- such as the ones made when designing tls-sni-*, which in this case turned out to be faulty -- and represents the one most likely to be futureproof. After all, what better way to prove you own a domain itself than being able to add arbitrary records to it that all nameservers then echo back?