Dunno about the protocol, but man, working with certbot and getting it do what I wanted was ... well, a lot more work than I would have guessed. The hooks system was so much trouble that I ended up writing my own.

But yeah, can definitely recommend DNS-01 over HTTP-01, since it doesn't involve implicitly messing with your server settings, and makes it much easier to have a single locked server with all the ACME secrets, and then distribute the certs to the open-to-the-internet web servers.