Running letsencrypt-auto is no different than running one of the curl | sh installers; they serve the same purpose. Getting you up and running under the assumption that you may be missing bits and pieces.
If you don't trust the official letsencrypt client, you can use this script to get your free certs. It doesn't install things or ask for sudo access or your private keys or have to be run on your server (except for one challenge response one-liner you can inspect). I wrote it specifically so people who didn't trust the letsencrypt client could still get free certs.
The best part is it doesn't need to bootstrap and try to install a bunch of dependencies that I don't want or need, unlike the official client.
Thanks a lot.