For the record, it is trivial to change PHPass to use $2y$ instead of $2a$. That said, this does require extending the PHPass class, so it is not ideal. Still, it would be better to extend or modify the class than it would be to simply try to roll your own (if those were your only two options).
Just to be clear, I didn't write the article, and I didn't recommend anything. If anything, it was posted as a discussion piece.
Well then the article is saying don't use $2a$ and then saying "oh but use this framework which also uses $2a$", which is terribly inconsistent. It should discuss when and where $2a$ could potentially be a problem.
Full steam ahead on the critique. I wanted to point out that you had no need to start bashing me about it!
Why would anyone recommend using bcrypt and then say to not use bcrypt ($2a$)?
Because you are technically supposed to use $2y$ which ensures you are not using the broken implementation that was fixed in 2011. Of course if you are using a newer php installation $2a$ will be identical to $2y$ so it's just a disambiguation, just as $2x$ is used to identify hashes generated using the broken implementation.