PA Semi didn’t do the A4. It was the existing VLSI team. Apple has made custom chips for years like the Northbridges for G4 and G5.
This information was appended to an article that focused on how great, and power-efficient, PA Semi's chip design really was. So why wouldn't Apple use them? Gizmodo speculates:
there likely isn't a whole lot "custom" going in the A4's actual design, which by all appearances is an ARM Cortex A9 wrapped up with a PowerVR graphics core and some other parts in a custom SoC. So, new question, if it's true: What's PA Semi, which Apple said would be working on chips for iPhones actually working on? A more customized chip would be interesting, since PA Semi's true talent was in designing chips with ridiculous power efficiencies.
So, we won't see PA Semi until... Apple A5?