I like to think that they are aimed at two different goals.
I wrote PHPXref over ten years ago as a quick hack to allow me to quickly and quickly learn the source code of a large project, without requiring a lot of tools (just Perl, and not even that, re on Windows) and without the need for a remote web server. Part of the documentation was a useful side effect, but in fact I just wanted a decent way to read through the source hyperlink in the browser.
PHPDocumentor .
PHPXref ( ), . - , , .