As stated in the Linux FHS standard http://refspecs.linuxfoundation.org/FHS_3.0/fhs/ch04s09.html
the /usr/local.bin directory is for local binaries. So scripts and programs local to the system for its users.
The /usr/local/sbin directory is for local system binaries. Since certbot and certbot-auto is not a regular user tool but for root/admin users it seems only logical to place them in /usr/local/sbin.
It also aids a little in the error messages about insecure permissions 9at least when you document the correct right settings).
Thanks for the feedback. You’re right that /usr/local/sbin more closely follows the Linux FHS, however, I don’t think we’re going to make this change because on some systems /usr/local/sbin isn’t in a user’s PATH by default (and you don’t need to invoke certbot-auto as root because it will help you reinvoke itself with su/sudo as needed). I personally don’t think opening this up as a potential problem for new sysadmins is worth changing our instructions.
With that said, the location of the certbot-auto script itself doesn’t matter as long as its permissions are secure. Feel free to place the file wherever you like!