> It munges your web server config (temporarily) to handle http challenges

I run it in "webroot" mode on NgINX servers so it's just a matter of including the relevant config file in your HTTP sections (likely before redirecting to HTTPS) so that "/.well-known/acme-challenge/" works correctly. Then when you do run certbot, it can put the challenge file into the webroot and NgINX will automatically serve it. This allows certbot to do its thing without needing to do anything with NgINX.