For anybody checking on this thread in the future,
certbot do the same thing and should be used interchangeably: if you installed Certbot via a tool like
emerge, or similar, then you have
certbot, while if you installed Certbot by downloading the script from EFF's web site with
wget, then you have
certbot-auto instead. Generally, each user will have one or the other depending on how they installed Certbot.
Whenever you see instructions anywhere that refer to one form, you should use the other form, if it's applicable to your system.
This is mentioned in EFF's documentation, but it's not repeated everywhere that example commands are given, and it's not necessarily mentioned at all in forum threads or other people's documentation.