There are two different phpbbcli.php files shipped with the full file download.  One is in the /bin directory and one is in the /install directory.  We have a KB article advising the use of the one in /bin ( e.g. https://www.phpbb.com/support/docs/en/3.2/ug/upgradeguide/upgrade3/ ), but I have also been told that the one in /install should be used.

Regardless of which is the case, would it not be better if both files were identical so whatever instructions a user was following, they would get the same result?

IOW, whichever is the proper file should be in both /bin and /install.