Hi Casey,
>> in what situations would an administrator want to use different folders?
short version: When they are already running a server on port 80.
longer version: when validating the domain from LetsEncrypt, LE will give you a file, and then make a request on port 80 to get that file back. You can have _any_ server on the machine on port 80 serve the file back. The AcmeFolder setting allows you to specify where the file should be on the machine so the "other" server can serve it to LE when requested.
cheers
Bruce