Or there is something missing from this passage:
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One of the drawbacks of the CGI version of PHP is its inability to use PHP-based authentication. Besides the overall performance hit, this would be the other glaring drawback. There's nothing, however, stopping you from using your normal Web server-based authentication; they're mutually exclusive.

Umm, she said carefully, I don't think there is. Given that I understand nothing about CGI and PHP, don't hold me to this, but: I think it's saying that CGI can't use PHP authorization, and therefore if you are required to get PHP authorization, then CGI will be no good for you. However, if your normal Web server-based authentication is acceptable, then CGI should/would be able to obtain this, since, if they are mutually exclusive, whatever it is about PHP that's preventing the authorization doesn't hold true for your regular server.

Woops--ignorance showing again. Should have put authentication, not authorization.