I read this article on the Apple site and tried to work with PHP with Project Builder for a while and found it just to be a kludge. A bit like using a pair of pliers to undo a nut...doable but not ideal!
There are little irritations that become major over time... One example; "directories" in the project browser are virtual and do not generate or delete actual directories in your OS. This forces the need to to and fro between OS and PB, reupdating etc...
As a closing example I posted to the official Apple PB mailing list asking if anyone ACTUALLY used PB for PHP work and got little response. That's a small indication that it's just not the best or even a particularly good tool for the job.
I decided to use jEdit ( http:www.jedit.org ) which although a little slow at times has abilities that make up for the lack of speed. BBEdit is also certainly a better choice.
I'd very much like Apple to make some adaptions to allow PHP work in PB as it is potentially very good for the job, but for now I'd suggest using something more suited.