There is a culture of not using libraries in PHP, because the built-in functionality is "good enough". People make the same mistakes again and again and again. (Just today there was a Rails "best practices" article saying how to roll your own salted digest authentication from scratch. WTF!?)
And anyway, I don't see a bcrypt implementation there. People will do what's easy; if it's as easy to do the (significantly more secure) bcrypt, they will. If it's easiest to do an unsalted MD5 digest, they will.
Someone certainly could write a library exactly like Authen::Passphrase for PHP or Ruby or whatever; but they haven't, so people do it wrong. They have gotten used to not having libraries, so they don't even look. (They search for blogs instead, and cut-n-paste years-old code. The culture practically insists on it.)